[cig-commits] r5567 - mc/3D/CitcomS/trunk
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Dec 8 16:26:39 PST 2006
Author: tan2
Date: 2006-12-08 16:26:38 -0800 (Fri, 08 Dec 2006)
New Revision: 5567
Modified:
mc/3D/CitcomS/trunk/ChangeLog
Log:
Regenerated ChangeLog upto r5565
Modified: mc/3D/CitcomS/trunk/ChangeLog
===================================================================
--- mc/3D/CitcomS/trunk/ChangeLog 2006-12-09 00:22:28 UTC (rev 5566)
+++ mc/3D/CitcomS/trunk/ChangeLog 2006-12-09 00:26:38 UTC (rev 5567)
@@ -1,3 +1,2907 @@
+2006-12-08 23:50 sue
+
+ * doc/manual/citcoms.lyx: small text changes; image resize
+
+2006-12-08 23:45 tan2
+
+ * doc/manual/citcoms.lyx: Added "created by OpenDX" on several
+ figure captions
+
+2006-12-08 23:36 tan2
+
+ * doc/manual/citcoms.lyx, doc/manual/graphics/mayavi2.png: Updated
+ MayaVi2 section
+
+2006-12-08 23:30 tan2
+
+ * visual/Makefile.am,
+ visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
+ visual/mayavi2_citcoms_display.py: Renamed the MayaVi launching
+ script and move it to visual/
+
+2006-12-08 23:26 tan2
+
+ * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Added
+ executable bit to file permission
+
+2006-12-08 22:44 luis
+
+ * visual/Makefile.am: Add plugins for MayaVi2 to installation
+
+2006-12-08 22:27 luis
+
+ * visual/Mayavi2/README, visual/Mayavi2/citcoms_display/README,
+ visual/Mayavi2/citcoms_plugins/README: Added README files
+
+2006-12-08 22:00 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size,
+ text size and other small text changes
+
+2006-12-08 21:16 luis
+
+ * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Removing
+ reduce filter from comments, as it is currently obsolete.
+
+2006-12-08 21:15 luis
+
+ * doc/manual/citcoms.lyx: Added MayaVi screenshot to manual, along
+ with a couple of other fixes.
+
+2006-12-08 20:03 luis
+
+ * visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py: Last
+ set of patches to citcoms_plugins * Display filename in mayavi
+ pipeline * Changed glob pattern so that only HDF5 timestep files
+ can be selected
+
+2006-12-08 19:47 luis
+
+ * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/citcoms_plugins/custom_ui.py,
+ visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsCapFilter.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsReduceFilter.py:
+ Forgot to rename data filters.
+
+2006-12-08 17:53 luis
+
+ * doc/manual/graphics/mayavi2.png: Added MayaVi2 screenshot for the
+ manual.
+
+2006-12-08 17:44 luis
+
+ * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/citcoms_plugins/custom_ui.py,
+ visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py,
+ visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py,
+ visual/Mayavi2/citcoms_plugins/utils.py: Various patches.
+
+2006-12-08 17:40 luis
+
+ * visual/Mayavi2/citcoms_plugins,
+ visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/citcoms_plugins/__init__.py,
+ visual/Mayavi2/citcoms_plugins/plugins,
+ visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py,
+ visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py,
+ visual/Mayavi2/citcoms_plugins/plugins/__init__.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSSphere.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowSurface.py,
+ visual/Mayavi2/citcoms_plugins/plugins/filter/__init__.py:
+ Forking original plugins
+
+2006-12-08 17:32 luis
+
+ * visual/Mayavi2/Martin, visual/Mayavi2/original_plugins,
+ visual/Mayavi2/original_plugins/README: Archiving original
+ plugins.
+
+2006-12-08 17:31 luis
+
+ * visual/Mayavi2/mayavi_custom_ui.py: Modify plugins directory
+
+2006-12-08 17:29 luis
+
+ * visual/Mayavi2/Martin/README: Explain contents of each directory.
+
+2006-12-08 02:29 leif
+
+ * configure.ac: Made 'install_deps' actually do what 'configure'
+ says it's doing (*missing* deps, not *all*).
+
+2006-12-07 23:26 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf,
+ doc/manual/graphics/regtest.100.z005.jpg: reinstated a few lost
+ changes; changed caption position on fig 5.3 on request; enlarged
+ fig 5.4; regen pdf
+
+2006-12-07 22:34 tan2
+
+ * doc/manual/citcoms.lyx: chapter 5 * Added MayaVi2 in the
+ introduction * Added links to MayaVi2 installation
+
+2006-12-07 22:19 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size;
+ regen pdf
+
+2006-12-07 22:09 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: text fixes to
+ recent additions
+
+2006-12-07 21:30 tan2
+
+ * doc/manual/citcoms.lyx, doc/manual/graphics/hdfview.png: * Put
+ back the HDFView sections * Added a screenshot of HDFView * Added
+ a warning on "-O3" compiler flag
+
+2006-12-07 05:03 sue
+
+ * doc/manual/citcoms.lyx: text edits to appendices and bib
+
+2006-12-07 00:12 sue
+
+ * doc/manual/citcoms.lyx: small changes to chapt 6; standardized
+ cross refference style; sstandardized code spacing
+
+2006-12-06 23:31 sue
+
+ * doc/manual/citcoms.lyx: enumerating several sections of the
+ instructions in chap 5 for clarity, and a few minor text fixes
+
+2006-12-06 20:59 sue
+
+ * doc/manual/citcoms.lyx: a few text fixes in chapter 3
+
+2006-12-06 20:33 sue
+
+ * doc/manual/citcoms.lyx: a few text fixes, preface to end of chapt
+ 2
+
+2006-12-06 18:59 sue
+
+ * doc/manual/citcoms.lyx: gurnis corrections and some other fixes
+
+2006-12-06 08:52 luis
+
+ * visual/Makefile.am: Temporarily removing Mayavi2 files from
+ Makefile.am
+
+2006-12-06 08:23 luis
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.c,
+ visual/Mayavi2/Citcoms_Hdf2Vtk.py,
+ visual/Mayavi2/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/Martin,
+ visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.c,
+ visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.py,
+ visual/Mayavi2/Martin/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/Martin/Citcoms_VtkDisplay.py,
+ visual/Mayavi2/Martin/README, visual/Mayavi2/Martin/__init__.py,
+ visual/Mayavi2/Martin/plugins, visual/Mayavi2/README,
+ visual/Mayavi2/__init__.py, visual/Mayavi2/plugins: Archive files
+ created during Martin Weier's internship
+
+2006-12-06 08:16 luis
+
+ * visual/Mayavi2/citcoms_display/plugins,
+ visual/Mayavi2/citcoms_display/plugins/HDF5FileReader.py,
+ visual/Mayavi2/citcoms_display/plugins/HDF5UGrid.py,
+ visual/Mayavi2/citcoms_display/plugins/ReduceFilter.py,
+ visual/Mayavi2/citcoms_display/plugins/ShowCapsFilter.py,
+ visual/Mayavi2/citcoms_display/plugins/ShowSurfaceFilter.py,
+ visual/Mayavi2/citcoms_display/plugins/Sphere.py,
+ visual/Mayavi2/citcoms_display/plugins/UGridThread.py,
+ visual/Mayavi2/citcoms_display/plugins/VTKFileReader.py,
+ visual/Mayavi2/citcoms_display/plugins/__init__.py: Reorganized
+ structure of the Mayavi2 plugin modules
+
+2006-12-06 08:13 luis
+
+ * visual/Mayavi2/citcoms_display/custom_ui.py,
+ visual/Mayavi2/citcoms_display/mayavi_custom_ui.py,
+ visual/Mayavi2/mayavi_custom_ui.py: Simplified the file that will
+ be be copied to user's ~/.mayavi2 directory.
+
+2006-12-06 06:55 luis
+
+ * visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Group all
+ CitcomS options under a single menu group.
+
+2006-12-06 05:58 luis
+
+ * doc/manual/citcoms.lyx: Quick fixes to manual.
+
+2006-12-06 01:08 leif
+
+ * CitcomS/Makefile.am, module/Regionalmodule.c, visual/Makefile.am:
+ Adding missing files to tarball ("make dist"), including the
+ 'Mayavi2' directory, which is now installed under share/CitcomS.
+ Also deleted 'Regionalmodule.c', which is no longer used.
+
+2006-12-06 00:49 sue
+
+ * doc/manual/citcoms.lyx: small changes in one image caption and in
+ citation
+
+2006-12-06 00:42 leif
+
+ * Makefile.am, bin/Makefile.am, configure.ac: Fix for eggs not
+ being installed by "make install" when builddir == srcdir. This
+ change also re-fixes the setup.py infinite regress in a cleaner
+ way.
+
+2006-12-06 00:18 luis
+
+ * visual/Mayavi2/citcoms_display/actions.py,
+ visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added actions
+ for ReduceFilter and ShowCapsFilter
+
+2006-12-05 23:13 leif
+
+ * Makefile.am, setup.py: Require final release version of Pythia.
+ Include egg-related files in release tarball ("make dist").
+
+2006-12-05 20:46 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: edited text and
+ images placement in 5.8
+
+2006-12-05 20:34 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: slghtly widened
+ l. col in appendix a tables as using typewriter widened lines;
+ fixed other formatting issues in appendices
+
+2006-12-05 20:11 sue
+
+ * doc/manual/citcoms.lyx: changing font style to typewriter small
+ in appendix a tablesi and a few typos
+
+2006-12-05 19:19 sue
+
+ * doc/manual/citcoms.lyx: small fixes to chap 4, text and table
+ placement
+
+2006-12-05 18:04 sue
+
+ * doc/manual/citcoms.lyx: making use of typewriter font and quotes
+ consistent in appendix a
+
+2006-12-05 07:09 tan2
+
+ * doc/manual/citcoms.lyx: Updated Chapter 4
+
+2006-12-05 06:17 tan2
+
+ * visual/samples/cookbook1.100.h5, visual/samples/cookbook1.h5:
+ Example h5 files including all optional output
+
+2006-12-05 06:14 tan2
+
+ * visual/Makefile.am: Forgot to update the makefile
+
+2006-12-05 05:04 tan2
+
+ * doc/manual/citcoms.lyx: Removed sections about HDFView.
+
+ HDFView by default displays the dataset in a 2D table, which can
+ be very confusing when working on multidimensional dataset.
+
+ "h5ls -r" is a better tool for discovering the group structure
+ and dataset dimension.
+
+2006-12-05 04:19 tan2
+
+ * visual/estimate.py, visual/estimate_size.py: * Renamed
+ estimate.py to estimate_size.py * Added license text * Update for
+ new HDF5 layout
+
+2006-12-05 00:46 luis
+
+ * doc/manual/citcoms.lyx: Changed code in A.1.1 and A.1.2 to use
+ small font with typewriter style.
+
+2006-12-05 00:40 tan2
+
+ * NEWS: Mentioned change of naming scheme for capfiles in NEWS
+
+2006-12-05 00:31 sue
+
+ * doc/manual/citcoms.lyx: fixed quotes; added degree symbols as
+ requested
+
+2006-12-05 00:14 tan2
+
+ * doc/manual/citcoms.lyx,
+ doc/manual/graphics/fulltest.xsect.100.jpg,
+ doc/manual/graphics/regtest.100.z005.jpg: Finished the GMT script
+ section
+
+2006-12-04 23:47 tan2
+
+ * visual/plot_annulus.py: Renamed "center" to "starting point"
+
+2006-12-04 22:42 sue
+
+ * doc/manual/citcoms.lyx: minor sentence/word form changes in 5.1
+ and 5.2
+
+2006-12-04 22:33 sue
+
+ * doc/manual/citcoms.lyx: reformatted column names in c.4.9
+
+2006-12-04 22:19 tan2
+
+ * doc/manual/citcoms.lyx: Revised Chapter 5 and Appendix A * Minor
+ revision of post-processing * Update OpenDX section for new HDF5
+ layout * Briefly mentioned GMT scripts (unfinished) * Described
+ new viscosity laws * Using Greek letter eta in the viscosity
+ equations
+
+2006-12-04 20:33 sue
+
+ * doc/manual/citcoms.lyx: fixed more quotes, fixed table breaks,
+ lines in table missing, other minor format problems
+
+2006-12-04 19:48 luis
+
+ * visual/Mayavi2/citcoms_display/__init__.py,
+ visual/Mayavi2/citcoms_display/actions.py,
+ visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added
+ OpenHDF5 and OpenVTK actions for mayavi2
+
+2006-12-04 17:24 luis
+
+ * doc/manual/citcoms.lyx: Fixes to manual
+
+2006-12-04 17:24 luis
+
+ * NEWS: Fixed typos
+
+2006-12-04 16:54 luis
+
+ * visual/h5tocap.c: Added vim modeline
+
+2006-12-04 14:21 luis
+
+ * visual/Mayavi2/citcoms_display/__init__.py,
+ visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Mayavi2 UI
+ customizations
+
+2006-12-04 14:11 luis
+
+ * visual/Mayavi2/citcoms_display: Added python module namespace for
+ the citcoms mayavi2 plugins
+
+2006-12-04 13:43 luis
+
+ * visual/Mayavi2/__init__.py,
+ visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
+ visual/Mayavi2/plugins/__init__.py,
+ visual/Mayavi2/plugins/filter/__init__.py: Removed executable
+ permissions
+
+2006-12-02 07:41 tan2
+
+ * doc/manual/graphics/CitcomSImportHDF5.net.gif,
+ visual/OpenDXMacro/CitcomSImportHDF5.net.in: Update for new HDF5
+ layout
+
+2006-12-02 07:14 tan2
+
+ * examples/Full/input.sample, examples/Regional/input.sample: *
+ Removed obsolete parameters * Added new parameters * Only one
+ "parameter=value" per line
+
+2006-12-02 06:04 tan2
+
+ * visual/h5tocap.c: Updated for new HDF5 layout
+
+2006-12-02 06:04 tan2
+
+ * visual/h5util.c, visual/h5util.h: Minor tweaks
+
+2006-12-02 04:43 tan2
+
+ * visual/Makefile.am, visual/h5tovelo.c, visual/h5util.c,
+ visual/h5util.h: Moved utility functions to h5util.c
+
+2006-12-02 04:15 tan2
+
+ * visual/h5tovelo.c: Fixed a bug of counting argc
+
+2006-12-02 00:57 tan2
+
+ * lib/Viscosity_structures.c: Added more rheology options, which is
+ required for benchmarks
+
+ rheol=1: visc = visc0 * exp(viscE * (viscT - T)) rheol=2: visc =
+ visc0 * exp(-T / viscT)
+
+2006-12-02 00:38 tan2
+
+ * visual/h5tocap.py: Updated h5tocap.py for new layout of HDF5
+ files
+
+2006-12-02 00:03 tan2
+
+ * visual/Makefile.am, visual/h5tovelo.c: Added a program to convert
+ h5 file to velo files for restart
+
+2006-12-01 23:34 sue
+
+ * doc/manual/citcoms.lyx: removed todo at 4.5.1, no issue there
+
+2006-12-01 22:00 leif
+
+ * configure.ac: Fix for infinite regress when builddir == srcdir.
+ !@#$%*
+
+ The .pth/sitedir/sys.path/PYTHONPATH aspect of eggs is really
+ irritating. I hope setuptools becomes a part of the standard
+ Python distro, as the Python core developers are likely to accept
+ it uncritically and unmodified (as they are wont to do,
+ apparently -- judging by all the other crap that is in the
+ standard library). God willing, this will further accelerate the
+ death of the language.
+
+2006-12-01 21:56 tan2
+
+ * visual/Makefile.am, visual/samples/cookbook1.100.h5,
+ visual/samples/cookbook1.h5: Added samples of HDF5 output
+
+2006-12-01 21:33 leif
+
+ * bin/Makefile.am, configure.ac: builddir != srcdir works again.
+
+ The use of setup.py/distutils/setuptools forces the creation of
+ files in srcdir. This bugs me.
+
+2006-12-01 04:40 leif
+
+ * Makefile.am, configure.ac: The "make install" command now works
+ again.
+
+2006-11-30 23:38 sue
+
+ * doc/manual/citcoms.lyx: fixed sentence in A.1.2 last row
+
+2006-11-30 23:08 tan2
+
+ * doc/manual/citcoms.lyx: Updated Chapter 6 * sync'd the manual
+ with the cookbook scripts * improving the resolution of
+ cookbook5.2.eps is left until the next release
+
+ Also, fixed table borders in Appendix A.
+
+2006-11-30 22:55 tan2
+
+ * examples/Cookbook5/cookbook5.cfg: Moved path name of restart file
+ to "datadir_old"
+
+2006-11-30 22:53 tan2
+
+ * examples/Cookbook1/cookbook1.cfg,
+ examples/Cookbook2/cookbook2.cfg,
+ examples/Cookbook3/cookbook3.cfg,
+ examples/Cookbook4/cookbook4.cfg,
+ examples/Cookbook5/cookbook5.cfg: Fixed issue63, Change
+ "monitoringfrequency" comment in citcoms cookbooks
+
+2006-11-30 22:21 luis
+
+ * doc/manual/citcoms.lyx: Done with Chapter 4 references.
+
+2006-11-30 21:16 tan2
+
+ * doc/manual/citcoms.lyx: The concept of caps is explained in
+ section 1.7
+
+2006-11-30 21:10 luis
+
+ * visual/Makefile.am, visual/h5steps.c: Removing obsolete program
+ h5steps.c
+
+2006-11-30 20:57 tan2
+
+ * doc/manual/citcoms.lyx: Updated Appendices
+
+2006-11-30 20:26 tan2
+
+ * doc/manual/citcoms.lyx: Updated section 3.6.1
+
+2006-11-28 23:28 leif
+
+ * CitcomS/Components/IC.py,
+ CitcomS/Components/Sphere/FullSphere.py,
+ CitcomS/Components/Sphere/RegionalSphere.py,
+ CitcomS/Solver/Solver.py, module/bindings.c,
+ module/getProperty.h, module/misc.c, module/misc.h,
+ module/setProperties.c: Fixed some bugs, some of which were
+ introduced during the C -> C++ transition.
+
+ Using a pidXXXX.cfg file as input should "work" now, although it
+ still doesn't reproduce the original simulation, since at least
+ one parameter is missing ('steps'). I maintain that dumping the
+ configuration is really the job of the framework (Pyre).
+ Unfortunately, Pyre's current capabilities in this area are buggy
+ in the case of '.pml' files, and non-existent in the case of
+ '.cfg' files.
+
+ Note: 'nproc_surf' is now a real inventory item, instead of a
+ fake one. It looks like it doesn't belong in the inventory at
+ all, though. (I left it there to avoid breakage.)
+
+2006-11-28 21:08 leif
+
+ * doc/manual/citcoms.lyx: Checked-in a virus, a worm, a Trojan
+ horse, and some other malware. LyX doesn't support copy & paste
+ between applications, so this check-in may have introduced some
+ bugs as well.
+
+2006-11-28 19:26 sue
+
+ * doc/manual/citcoms.lyx: various edits to 3.6.1 and 3.7
+
+2006-11-28 07:33 leif
+
+ * lib/Instructions.c: Rewrote expand_str() in order to: 1) avoid
+ potential buffer overflow; 2) avoid the use of non-standard
+ strndup(); 3) avoid the use of the heap altogether. (Prompted by
+ unresolved strndup on Mac OS X.)
+
+2006-11-28 05:00 tan2
+
+ * examples/Cookbook2/cookbook2.cfg: Clarified the comment
+
+2006-11-28 04:42 tan2
+
+ * NEWS: Updated for new features
+
+2006-11-28 04:41 tan2
+
+ * README: Added a reference to NEWS
+
+2006-11-28 03:34 tan2
+
+ * doc/manual/citcoms.lyx: Chapter 3 updated
+
+2006-11-28 03:01 leif
+
+ * CitcomS/CoupledApp.py, CitcomS/SimpleApp.py, bin/citcoms.in,
+ setup.py: Changes related to Pythia v0.8.1.0b7, which CitcomS now
+ requires: 'journal' is no longer a part of an application's
+ inventory, and pyre.applications.start() is now responsible for
+ calling run().
+
+2006-11-28 02:57 tan2
+
+ * examples/Cookbook6/cookbook6.cfg, examples/Full/input.sample,
+ examples/Regional/input.sample: Updated the dimensional const
+
+2006-11-28 02:55 tan2
+
+ * examples/example1.cfg: Updated to be consistent with the manual
+
+2006-11-27 23:09 tan2
+
+ * CitcomS/Solver/Solver.py, lib/Instructions.c: Changed the default
+ value of "datadir" to "."
+
+2006-11-27 22:37 tan2
+
+ * visual/Makefile.am, visual/autocombine.py,
+ visual/batchcombine.py, visual/batchpaste.sh,
+ visual/batchpaste2.sh, visual/execpaste.py: Changed
+ postprocessing scripts for the new "datadir" parameter
+
+2006-11-27 21:27 tan2
+
+ * visual/pasteCitcomData.sh: Fix for POSIX-compliant arithmetic
+ expression
+
+ The "sh" shell on my Ubuntu 6.10 doesn't have the "let" command.
+ That's how I found that "let" is not in the POSIX standard. Use
+ "$((expression))" instead.
+
+2006-11-27 20:05 tan2
+
+ * visual/citcoms_datadir: Added extern program to determine
+ "datadir"
+
+2006-11-27 20:05 tan2
+
+ * CitcomS/Components/Output.py, CitcomS/Solver/Solver.py,
+ lib/Instructions.c, lib/Output.c, lib/global_defs.h,
+ module/setProperties.c: Changes how to specify output directory
+
+ * "output_format" must be either "ascii" (the default) or "hdf5",
+ the "ascii-local" option is gone * "datafile" becomes the prefix
+ of the filename and cannot contain "/" * "datadir" becomes
+ mandatory input parameters * If "datadir" is "%DATADIR", the
+ output directory is determined by an external program
+ "citcoms_datadir" * Special substrings "%RANK", "%HOSTNAME" in
+ datadir will be substituted by mpi rank, machine's hostname,
+ $DATADIR environment variable, respectively. * These special
+ strings start with "%", rather than "$", becuase it's very
+ difficult to input "$" from the command line.
+
+2006-11-22 21:26 tan2
+
+ * lib/Stokes_flow_Incomp.c: Changed the convergence criterion of
+ Stokes solver: * stop iterations if delta(v) or delta(p) becomes
+ too small (i.e., v or p has converged) * this is suggested by
+ Shijie Zhong
+
+2006-11-22 21:25 tan2
+
+ * lib/Full_parallel_related.c: Ignoring overlapping nodes when
+ counting # of global nodes
+
+2006-11-22 20:25 sue
+
+ * doc/manual/citcoms.lyx: typo; made references into an itemized
+ list
+
+2006-11-22 20:05 tan2
+
+ * lib/Full_parallel_related.c, lib/Full_version_dependent.c,
+ lib/Makefile.am, lib/Regional_parallel_related.c,
+ lib/Regional_version_dependent.c, lib/global_defs.h,
+ lib/temperature_descriptions.h: Removed unused codes and files
+
+2006-11-22 19:41 tan2
+
+ * lib/Output.c, lib/Output_h5.c, lib/Sphere_harmonics.c,
+ lib/Topo_gravity.c, lib/global_defs.h: Refactored geoid
+ calculation
+
+2006-11-21 23:03 luis
+
+ * doc/manual/citcoms.lyx: Expanded section on optimizing parallel
+ I/O.
+
+2006-11-21 20:18 tan2
+
+ * visual/plot_annulus.py, visual/plot_layer.py, visual/zslice.py:
+ Added scripts for 2D temperature plots, using GMT commands
+
+2006-11-20 19:24 tan2
+
+ * lib/Sphere_harmonics.c: Forgot to declare function prototype
+
+2006-11-18 05:17 tan2
+
+ * lib/Sphere_harmonics.c: Disabled a debugging output, which is not
+ protected by a "if(E->control.verbose)" and caused Segmentation
+ Fault.
+
+2006-11-18 01:29 leif
+
+ * bin/pycitcoms.c: The function loadObject() has been moved from
+ Pythia to Merlin.
+
+2006-11-18 00:48 tan2
+
+ * examples/Full/input.sample, examples/Full/velbc/README,
+ examples/Full/velbc/velbc_full.tar.gz, examples/Makefile.am:
+ Updated the vbc files and input file
+
+2006-11-18 00:41 tan2
+
+ * examples/Regional/input.sample, examples/Regional/velbc/README,
+ examples/Regional/velbc/velbc_regional.tar.gz,
+ examples/Regional/velbc/velbc_regional40,
+ examples/Regional/velbc/velbc_regional41: Updated the vbc files
+ and input file.
+
+2006-11-18 00:20 tan2
+
+ * lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h,
+ lib/output_h5.h: HDF5 output for geoid is working
+
+2006-11-17 22:37 luis
+
+ * ., CitcomS, bin, etc, examples, lib, module, tests, visual,
+ visual/OpenDXMacro: Cleaned up 'svn status' by updating
+ svn:ignore property
+
+2006-11-17 20:25 tan2
+
+ * lib/Output_h5.c: HDF5 output of surf, botm, horiz_avg are working
+ now.
+
+ * Time and timestep infomation is written as scalar attributes
+ "time" and "timestep" in / group. * Set MPI_Info according to
+ input parameters "cb_block_size" and "cb_buffer_size" * I decided
+ not to write surf, botm, and horiz_avg coordinates. This
+ coordinate can be retrieved from the 3D coordinate very easily by
+ this pseudo-code: surf_coord = coord[cap=all, x=all, y=all, z=1]
+ z_coord = coord[cap=1, x=1, y=1, z=all]
+
+ Remainging works: geoid for hdf5, update the manual
+
+2006-11-17 06:26 tan2
+
+ * lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h,
+ lib/output_h5.h: HDF5 output reloaded. See issue4 for reasoning.
+
+ Most data outputs are working. Remaining works: * How to deal
+ with time output? (Maybe not output at all? Time info is always
+ written in the .time file anyway.) * Where to put 2d and 1d
+ coordinate output? (Maybe output with the data? These datasets
+ are small and won't take too much space anyway.) * Geoid output
+
+2006-11-17 05:34 leif
+
+ * CitcomS/Components/Output.py: Fixed a minor bug in Output.py.
+
+2006-11-17 02:24 leif
+
+ * doc/manual/citcoms.lyx: Revised everything having to do with
+ runtime configuration: launcher.xxx, scheduler.xxx, and job.xxx.
+
+ Lowered the prominence/importance given to .pml files... and
+ resisted my temptation to delete all reference to them :-)
+
+ (I think I'm pretty much done with the v2.1 manual at this point.
+ Reading the manual makes me tired, because it reminds me of how
+ much work remains to be done on the code itself. Ease-of-use
+ could be substantially improved...)
+
+2006-11-16 21:58 leif
+
+ * bin/Makefile.am: Reverted another recent decision of mine: Always
+ build the legacy drivers, 'CitcomSFull' and 'CitcomSRegional'. I
+ took these out of the Pyre build to avoid confusion; but now --
+ thinking of shared installations of CitcomS on clusters -- I
+ think they should always be built (as they were before) so that
+ users have the option.
+
+2006-11-16 21:36 leif
+
+ * examples/Makefile.am: Install examples under
+ PREFIX/share/CitcomS/examples, as now documented in the manual.
+ This is for the benefit of users of shared installations of
+ CitcomS. I also sync'd the file list in examples/Makefile.am.
+
+ Note: the file velbc_regional.tar.gz seems to be corrupt!!!
+
+2006-11-16 21:25 leif
+
+ * doc/manual/citcoms.lyx: Corrections with respect to r5302: the
+ binaries/scripts are now once again built under the 'bin'
+ subdirectory.
+
+ Also reviewed all references to PREFIX.
+
+2006-11-16 14:40 leif
+
+ * Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am, bin,
+ bin/Citcom.c, bin/CitcomSFull.c, bin/CitcomSRegional.c,
+ bin/Makefile.am, bin/citcoms.in, bin/pycitcoms.c, citcoms.in,
+ configure.ac, pycitcoms.c: Re-created 'bin' subdirectory to avoid
+ filename conflict on case-sensitive filesystems (Mac, Windows):
+ "CitcomS" == "citcoms".
+
+ Fixed egg-related bugs which prevented 'configure' from
+ succeeding when buildir != srcdir (another BuildBot test vector).
+
+ Call addsitedir() in the 'citcoms' script. I guess this is now
+ necessary since "site.py" is no longer in the same directory as
+ "citcoms". (*)
+
+ Note that there is currently a bug in Merlin which prevents
+ 'citcoms' from running ("No module named pkg_resources"). The
+ work-around is to manually add the merlin egg to the
+ merlin-install.pth file.
+
+ There are more bugs which prevent running on Mac OS X at all
+ (still investigating).
+
+ (*) I'm becoming annoyed with setuptools' use of .pth files as a
+ sys.path/PYTHONPATH persistence mechanism, mainly because of the
+ accompanying hacks which are used to turn ordinary directories
+ into "site" directories (i.e., directories where .pth files work)
+ -- these ugly, confusing hacks include the fake site.py, "virtual
+ python", etc. I think Merlin will only use .pth files in real
+ site directories. It will use clear, straitforward, direct
+ sys.path manipulation everywhere else.
+
+2006-11-16 03:04 tan2
+
+ * module/setProperties.c: Forgot to commit module/ directory
+
+2006-11-16 03:01 tan2
+
+ * lib/Topo_gravity.c: Declared function prototype at the top
+
+2006-11-16 02:07 tan2
+
+ * CitcomS/Components/Const.py, CitcomS/Components/Output.py,
+ CitcomS/Components/Sphere/Sphere.py: Forgot to commit python
+ files
+
+2006-11-16 02:07 tan2
+
+ * lib/Sphere_harmonics.c: Declared function prototype at the top
+
+2006-11-16 01:52 tan2
+
+ * lib/Element_calculations.c, lib/Full_obsolete.c,
+ lib/Full_parallel_related.c, lib/Full_version_dependent.c,
+ lib/General_matrix_functions.c, lib/Global_operations.c,
+ lib/Instructions.c, lib/Obsolete.c, lib/Output.c,
+ lib/Output_h5.c, lib/Regional_obsolete.c,
+ lib/Regional_parallel_related.c,
+ lib/Regional_version_dependent.c, lib/Sphere_harmonics.c,
+ lib/Topo_gravity.c, lib/global_defs.h: Implemented geoid
+ calculation, see issue64. User visible changes include: *
+ "output_optional" can include string "geoid", which will enable
+ geoid output * new input parameters: radius, density_above,
+ density_below * removed input parameters: layerd, wdensity,
+ llmax, nlong, nlati * moved input parameter "output_ll_max" from
+ Sphere.py to Output.py * sync'd the defalut values of input
+ parameters in Const.py and Instructions.c
+
+ TODO: h5output_geoid() not finished
+
+2006-11-15 22:01 leif
+
+ * doc/manual/citcoms.lyx: Elaborated a bit on .egg download, and
+ clarified that CitcomS needs Pythia v0.8.1.x (instead of 0.8).
+
+2006-11-15 21:18 leif
+
+ * doc/manual/citcoms.lyx: Re-read the stuff I worked on yesterday,
+ making minor corrections: "is in your PATH" -> "is on your PATH",
+ inserted the word "Section" before section references, other
+ minor changes.
+
+2006-11-15 20:40 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: a few typos
+ fixed, http removed from htmlurl tags (not needed and lengthen
+ name in line); pdf regen
+
+2006-11-15 02:06 leif
+
+ * doc/manual/citcoms.lyx: Corrections to the section, "Changing
+ Parameters".
+
+2006-11-15 01:14 leif
+
+ * doc/manual/citcoms.lyx: Updated the installation chapter.
+
+2006-11-14 03:25 leif
+
+ * Makefile.am, citcoms.in, pycitcoms.c, setup.py: Pythia
+ v0.8.1.0b4: Fixed bugs relating to MPI launching: Fix
+ sys.path/PYTHONPATH automatically; don't touch 'argv' until after
+ MPI_Init().
+
+ Next, I may try to slurp 'pycitcoms.c' into the framework... it
+ contains a lot of implementation details which have everything to
+ do with Pyre and nothing to do with CitcomS.
+
+2006-11-11 03:34 leif
+
+ * ., configure.ac, ez_setup.py, setup.py: Use the new merlin (the
+ setuptools clone). Download Python dependencies automatically
+ during 'configure' (This doesn't work for "make install" yet.)
+
+ The Dynamo BuildBot might even succeed after this check-in...
+ fingers crossed...
+
+2006-11-10 19:20 sue
+
+ * doc/manual/citcoms.lyx: created formulas for sec a.1.11
+
+2006-11-10 18:54 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/graphics/cookbook7.eps:
+ cookbook 6 graphic edited, various small tweaks
+
+2006-11-10 01:59 sue
+
+ * doc/manual/citcoms.lyx: finished various typos and fixes after
+ checking with Luis on questions
+
+2006-11-09 19:37 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms_cover-layers.pdf,
+ doc/manual/citcoms_cover.pdf, doc/manual/graphics/c_fig1.eps:
+ various typos and fixes
+
+2006-11-07 19:33 tan2
+
+ * doc/manual/citcoms.lyx: * Fixed a few typos * Added "TODO" in
+ front of all unfinished text.
+
+2006-11-07 02:30 leif
+
+ * Makefile.am, configure.ac, lib/Makefile.am, visual/Makefile.am:
+ Moved CitcomS HDF5 macros to cs/autoconf.
+
+2006-11-07 01:33 leif
+
+ * ., CitcomS/Makefile.am, Makefile.am, bin, citcoms.in,
+ configure.ac, etc/Makefile.am, lib/Makefile.am, module/Exchanger,
+ module/Makefile.am, project.cfg, pycitcoms.c, setup.py,
+ visual/Makefile.am: Took a step backwards so that I can take a
+ more conservative approach to build/install. Also, temporarily
+ deleted 'Exchanger' and all references to it, to avoid confusion.
+ We can always go back in time and retrieve it later.
+
+2006-11-07 00:49 sue
+
+ * doc/manual/citcoms.pdf: pdf generated
+
+2006-11-07 00:49 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/graphics/c_fig1.eps,
+ doc/manual/graphics/cookbook1.eps,
+ doc/manual/graphics/cookbook2.eps: gurnis edits, new pdf
+
+2006-11-06 18:53 sue
+
+ * doc/manual/citcoms.lyx,
+ doc/manual/graphics/citcoms_cover-layers.pdf,
+ doc/manual/graphics/citcoms_cover.pdf: added authors to cover
+
+2006-11-06 18:33 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/graphics/proc_mesh.eps: added
+ new section 1.7 per gurnis and supporting graphic
+
+2006-11-01 20:47 luis
+
+ * doc/manual/citcoms.lyx: Re-typed most of the changes from my copy
+ of the citcoms.lyx file
+
+2006-10-27 21:26 tan2
+
+ * tests/.cvsignore: Removed legacy file .cvsignore
+
+2006-10-27 21:25 tan2
+
+ * doc/.cvsignore: Removed legary file .cvsignore
+
+2006-10-20 19:36 tan2
+
+ * examples/.reset-temporary: This file (examples/.reset-temporary)
+ was checked into svn at the initial import by me. I don't
+ remember what this file was used for.
+
+2006-10-20 19:00 tan2
+
+ * CitcomS/Solver/Solver.py: * Removed extra output_time(), which
+ was used for profiling * Converted tab to 4 spaces
+
+2006-10-20 08:19 leif
+
+ * configure.ac: Fail if MPI lib/header is not found.
+
+2006-10-17 11:00 leif
+
+ * CitcomS/Makefile.am, Makefile.am, bin/Makefile.am,
+ etc/Makefile.am, lib/Makefile.am, module/Makefile.am: Fixed
+ legacy build.
+
+2006-10-17 09:18 leif
+
+ * ., Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am,
+ bin/Citcom.c, configure.ac, doc/CitComS.doxyconf,
+ lib/Pan_problem_misc_functions.c, lib/Tracer_advection.c,
+ module/CitcomSmodule.c, module/Makefile.am,
+ module/Regionalmodule.c, module/advdiffu.c, module/bindings.c,
+ module/exceptions.c, module/initial_conditions.c,
+ module/mesher.c, module/misc.c, module/outputs.c,
+ module/setProperties.c, module/stokes_solver.c, project.cfg,
+ setup.py, tests/Makefile.am, visual/Makefile.am: Transitioning to
+ Merlin. (Warning: still under construction.)
+
+2006-10-14 00:29 tan2
+
+ * CitcomS/Solver/CoupledSolver.py: Undid the accidental checkin at
+ r4998
+
+2006-10-14 00:27 tan2
+
+ * CitcomS/Solver/Solver.py, doc/manual/citcoms.lyx,
+ lib/Instructions.c, lib/Output.c, lib/Output_h5.c,
+ lib/global_defs.h, visual/estimate.py: Renamed reference of
+ "average" to "horiz_avg"
+
+2006-10-14 00:06 tan2
+
+ * NEWS: Added description on new features and bug fixes for v2.1.0
+
+2006-10-13 23:59 luis
+
+ * lib/Output_h5.c: Settled on /horiz_avg/ instead of /have/
+
+2006-10-13 23:46 sue
+
+ * doc/manual/citcoms.lyx: updated url handling
+
+2006-10-13 23:18 tan2
+
+ * visual/h5tocap.c: * Updated for the new layout of HDF5 group *
+ Changed the order of nodes, so that the output is the same as the
+ cap file from autocombine.py
+
+2006-10-13 07:39 tan2
+
+ * doc/manual/citcoms.lyx: * Fixed a typo "PHDF HOME" -> "PHDF_HOME"
+ * Added a section on using none-pyre version * Undid a xref in
+ section 3.1, which should link to (not-checked-in-yet) "Working
+ with HDF5" chapter * Updated Appendix A and changed the title *
+ Added description on new output files (stress, pressure, average)
+
+2006-10-13 06:43 tan2
+
+ * lib/Full_geometry_cartesian.c, lib/Regional_geometry_cartesian.c,
+ lib/Viscosity_structures.c: Gave default values to several
+ parameters
+
+2006-10-13 04:15 tan2
+
+ * examples/Full/input.sample, examples/Regional/input.sample:
+ Removed obsolete input parameter "maxadvtime" from the input
+ samples
+
+2006-10-13 04:10 tan2
+
+ * CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
+ CitcomS/Components/Stokes_solver/Incompressible.py,
+ lib/Output_h5.c, module/setProperties.c: Moved input parameters
+ "aug_lagr" and "aug_number" from tsolver to vsolver, where they
+ really should belong to. These parameters are for augmented
+ lagragian stiffness matrix (I have no idea on what it is...), as
+ indicated in Element_calculations.c.
+
+2006-10-12 21:43 tan2
+
+ * CitcomS/Components/IC.py, module/setProperties.c:
+ 'half_space_age' was not used when 'tic_method'=1. So, fixed the
+ comment and removed the conditional input
+
+2006-10-12 14:48 leif
+
+ * CitcomS/BaseApplication.py,
+ CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
+ CitcomS/Components/BC.py, CitcomS/Components/CitcomComponent.py,
+ CitcomS/Components/CodecConfig.py, CitcomS/Components/Const.py,
+ CitcomS/Components/HackedConfigParser.py,
+ CitcomS/Components/IC.py, CitcomS/Components/Launchers.py,
+ CitcomS/Components/Output.py, CitcomS/Components/Param.py,
+ CitcomS/Components/Phase.py, CitcomS/Components/Sphere/Sphere.py,
+ CitcomS/Components/Stokes_solver/Incompressible.py,
+ CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py,
+ CitcomS/CoupledApp.py, CitcomS/SimpleApp.py,
+ CitcomS/Solver/Solver.py, bin/Citcom.c, bin/Makefile.am,
+ bin/citcoms.in, bin/coupledcitcoms.in, bin/pycitcoms.c,
+ bin/pycitcoms.cc, bin/pycppcitcoms.cc, configure.ac,
+ doc/manual/citcoms.lyx, etc/CitcomS.pml.in, etc/Makefile.am,
+ etc/globus.odb, etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb,
+ etc/pbs.odb, lib/Advection_diffusion.c, lib/Citcom_init.c,
+ lib/Drive_solvers.c, lib/Full_parallel_related.c,
+ lib/Full_version_dependent.c, lib/Global_operations.c,
+ lib/Instructions.c, lib/Lith_age.c, lib/Output.c,
+ lib/Output_h5.c, lib/Parsing.c, lib/Process_buoyancy.c,
+ lib/Regional_parallel_related.c,
+ lib/Regional_version_dependent.c, lib/Topo_gravity.c,
+ lib/Tracer_advection.c, lib/global_defs.h,
+ lib/sphere_communication.h, module/CitcomSmodule.c,
+ module/CitcomSmodule.cc, module/CitcomSmodule.h,
+ module/Makefile.am, module/PyxMPI, module/Regionalmodule.c,
+ module/Regionalmodule.cc, module/advdiffu.c, module/advdiffu.cc,
+ module/advdiffu.h, module/bindings.c, module/bindings.cc,
+ module/bindings.h, module/exceptions.c, module/exceptions.cc,
+ module/exceptions.h, module/getProperty.h,
+ module/initial_conditions.c, module/initial_conditions.cc,
+ module/initial_conditions.h, module/mesher.c, module/mesher.cc,
+ module/mesher.h, module/misc.c, module/misc.cc, module/misc.h,
+ module/outputs.c, module/outputs.cc, module/outputs.h,
+ module/setProperties.c, module/setProperties.cc,
+ module/setProperties.h, module/stokes_solver.c,
+ module/stokes_solver.cc, module/stokes_solver.h, setup.py: Moved
+ 'launcher' and '.cfg' support out of CitcomS and into the
+ framework.
+
+ As I was revising the "Installation" chapter of the manual (still
+ in progress), I got frustrated with how complicated everything
+ was -- and how difficult it was to document that complexity -- so
+ I did something slightly violent:
+
+ Converted the CitcomS extension module, 'CitcomSLib', from C++ to
+ C. This is made possible by Pythia 0.8.1.0b2, which replaces
+ _mpimodule with _mpi.pyx, which has a C interface.
+
+ It is now possible to build CitcomS -- and all its prerequisites
+ (e.g. Python) -- entirely from source, starting with nothing but
+ a C compiler. Exchanger still requires C++, of course. I have yet
+ to test these changes with Exchanger enabled, but I don't
+ anticipate any serious problems.
+
+ This may have been overkill, but I also cleaned the source of
+ C++-style comments (even though most modern C compilers probably
+ accept them... it became standard in C99 or something).
+
+ I'll bet you can install CitcomS with GCC 2.x now :-)
+
+2006-10-11 20:01 sue
+
+ * doc/manual/citcoms.lyx: took care of some todo items
+
+2006-10-10 23:48 tan2
+
+ * doc/manual/citcoms.lyx: * Added subsection on installing
+ OpenDXutils package * Aligned figures to the center * Changed the
+ layout of the Appendices
+
+2006-10-10 20:37 sue
+
+ * doc/manual/citcoms.lyx: added hdf5 install and addt tools
+ chapters
+
+2006-10-10 18:42 luis
+
+ * doc/manual/citcoms.lyx: Inserted a few TODO items
+
+2006-10-10 13:00 luis
+
+ * lib/Makefile.am, lib/Output_h5.c, lib/PyTables.c, lib/pytables.h:
+ 1. Reorganized routines in a more logical order. 2. Consolidated
+ routines from PyTables.[ch] into Output_h5.c
+
+2006-10-10 11:54 luis
+
+ * lib/Instructions.c, lib/Output_h5.c, lib/output_h5.h: Renamed
+ local function to conform with h5 prefix.
+
+2006-10-10 07:29 luis
+
+ * lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: 1. Added PID to
+ metadata to make it easier to identify the corresponding .cfg
+ file 2. Wrapped most calls to set_attribute() to avoid using
+ addresses as arguments 3. Added
+ set_attribute_{int,float,double}_vector() functions
+
+2006-10-10 00:52 luis
+
+ * lib/Output_h5.c: Forgot to delete reference to obsolete
+ data_group.
+
+2006-10-10 00:52 tan2
+
+ * doc/manual/citcoms_cover-layers.pdf,
+ doc/manual/citcoms_cover.pdf: Set MIME type to pdf
+
+2006-10-10 00:51 tan2
+
+ * doc/manual/graphics/CitcomSImportHDF5.net.gif: Set MIME type to
+ image
+
+2006-10-10 00:48 tan2
+
+ * doc/manual/graphics/c_fig1.eps, doc/manual/graphics/c_fig10.eps,
+ doc/manual/graphics/c_fig2.eps, doc/manual/graphics/c_fig3.jpg,
+ doc/manual/graphics/c_fig4.eps, doc/manual/graphics/c_fig5.eps,
+ doc/manual/graphics/c_fig6.jpg, doc/manual/graphics/c_fig7.eps,
+ doc/manual/graphics/c_fig8.eps, doc/manual/graphics/c_fig9.eps,
+ doc/manual/graphics/cookbook1.2.jpg,
+ doc/manual/graphics/cookbook1.eps,
+ doc/manual/graphics/cookbook1.png,
+ doc/manual/graphics/cookbook2.2.eps,
+ doc/manual/graphics/cookbook2.2eps,
+ doc/manual/graphics/cookbook2.eps,
+ doc/manual/graphics/cookbook3.eps,
+ doc/manual/graphics/cookbook4.eps,
+ doc/manual/graphics/cookbook5.2.eps,
+ doc/manual/graphics/cookbook5.eps,
+ doc/manual/graphics/cookbook6.2.eps,
+ doc/manual/graphics/cookbook6.eps,
+ doc/manual/graphics/cookbook7.eps: Set MIME type to image
+
+2006-10-10 00:45 luis
+
+ * lib/Output_h5.c: Shortened /average/ group into /have/
+
+2006-10-10 00:42 tan2
+
+ * doc/manual/graphics/CitcomSImportHDF5.net.gif: Figure for HDF5
+ visualization
+
+2006-10-10 00:41 tan2
+
+ * doc/manual/citcoms.lyx: Added section on visualizing HDF5 output
+
+2006-10-10 00:38 luis
+
+ * lib/Output_h5.c: Fix mispelling in input parameters (allignment
+ options).
+
+2006-10-09 23:25 tan2
+
+ * doc/manual/citcoms.lyx: * Added documentaion of .pml file, which
+ comes from DANSE FAQ * Added section on visualization of full
+ version * Moved the discussion on .log and .time files from
+ Section 4.2 to Section 3.5.3 * Updated links to equations
+
+2006-10-09 23:14 sue
+
+ * doc/manual/citcoms.lyx: change equation numbering
+
+2006-10-09 20:41 tan2
+
+ * visual/OpenDXMacro/CitcomSImportHDF5.net.in: Changed the order of
+ input parameters
+
+2006-10-09 19:58 tan2
+
+ * visual/OpenDXMacro/CitcomSImportHDF5.net.in: Updated for the new
+ layout of hdf5 output
+
+2006-10-09 00:14 gurnis
+
+ * lib/Full_read_input_from_files.c, lib/Problem_related.c,
+ lib/Viscosity_structures.c: For Viscosity_structures.c, added a
+ new rheology, rheol=5, that is a variant of rheol=3. The
+ difference lay in the way that plate boundaries are weakened.
+ Must set mat_control=1 and enter materials into the VIP array.
+ Removed debug statements from Problem_related.c in preparation of
+ new release.
+
+2006-10-08 12:04 leif
+
+ * configure.ac, setup.py: Pointed CitcomS egg-downloading at the
+ new "Eggs" section on the web site, to insulate CitcomS from the
+ imminent chaos in pythia-dev.
+
+2006-10-07 01:15 tan2
+
+ * visual/h5tocap.py: Updated for the new layout in the h5 file
+
+2006-10-07 00:01 luis
+
+ * lib/Output_h5.c: Eliminated data group in HDF5 file. Main
+ datasets are now on the root-level.
+
+2006-10-06 21:10 tan2
+
+ * lib/Obsolete.c: The type of elt_g should be "higher_precision"
+ instead of "double".
+
+2006-10-06 20:18 tan2
+
+ * lib/Interuption.c: Changed the signature of the signal handler
+ from (void)(interuption(void)) to (void)(interuption(int)) to
+ conform with the C standard
+
+2006-10-06 20:02 tan2
+
+ * lib/element_definitions.h: Missing braces around initializers for
+ array structs node_point[] and offset[]
+
+2006-10-06 17:17 tan2
+
+ * doc/manual/citcoms.lyx: Some minor edits
+
+2006-10-05 20:07 tan2
+
+ * visual/combine.py: Using 2-digit number for the cap filename, eg.
+ prefix.cap00.step
+
+2006-10-05 00:38 tan2
+
+ * visual/visFull.cfg, visual/visFull.net.in,
+ visual/visRegional.cfg, visual/visRegional.net.in: Updated macros
+ to use new samples files and fixed a few stylus issues
+
+2006-10-05 00:15 tan2
+
+ * visual/Makefile.am: Rearranged file list
+
+2006-10-05 00:15 tan2
+
+ * visual/Makefile.am: Updated file list
+
+2006-10-05 00:04 tan2
+
+ * visual/samples/fulltest.cap0.0,
+ visual/samples/fulltest.cap0.0.general,
+ visual/samples/fulltest.cap00.100,
+ visual/samples/fulltest.cap00.100.general,
+ visual/samples/fulltest.cap01.100,
+ visual/samples/fulltest.cap01.100.general,
+ visual/samples/fulltest.cap02.100,
+ visual/samples/fulltest.cap02.100.general,
+ visual/samples/fulltest.cap03.100,
+ visual/samples/fulltest.cap03.100.general,
+ visual/samples/fulltest.cap04.100,
+ visual/samples/fulltest.cap04.100.general,
+ visual/samples/fulltest.cap05.100,
+ visual/samples/fulltest.cap05.100.general,
+ visual/samples/fulltest.cap06.100,
+ visual/samples/fulltest.cap06.100.general,
+ visual/samples/fulltest.cap07.100,
+ visual/samples/fulltest.cap07.100.general,
+ visual/samples/fulltest.cap08.100,
+ visual/samples/fulltest.cap08.100.general,
+ visual/samples/fulltest.cap09.100,
+ visual/samples/fulltest.cap09.100.general,
+ visual/samples/fulltest.cap1.0,
+ visual/samples/fulltest.cap1.0.general,
+ visual/samples/fulltest.cap10.0,
+ visual/samples/fulltest.cap10.0.general,
+ visual/samples/fulltest.cap10.100,
+ visual/samples/fulltest.cap10.100.general,
+ visual/samples/fulltest.cap11.0,
+ visual/samples/fulltest.cap11.0.general,
+ visual/samples/fulltest.cap11.100,
+ visual/samples/fulltest.cap11.100.general,
+ visual/samples/fulltest.cap2.0,
+ visual/samples/fulltest.cap2.0.general,
+ visual/samples/fulltest.cap3.0,
+ visual/samples/fulltest.cap3.0.general,
+ visual/samples/fulltest.cap4.0,
+ visual/samples/fulltest.cap4.0.general,
+ visual/samples/fulltest.cap5.0,
+ visual/samples/fulltest.cap5.0.general,
+ visual/samples/fulltest.cap6.0,
+ visual/samples/fulltest.cap6.0.general,
+ visual/samples/fulltest.cap7.0,
+ visual/samples/fulltest.cap7.0.general,
+ visual/samples/fulltest.cap8.0,
+ visual/samples/fulltest.cap8.0.general,
+ visual/samples/fulltest.cap9.0,
+ visual/samples/fulltest.cap9.0.general,
+ visual/samples/regtest.cap0.0,
+ visual/samples/regtest.cap0.0.general,
+ visual/samples/regtest.cap00.100,
+ visual/samples/regtest.cap00.100.general: Replaced sample files
+ at 0th time step with sample files at 100th time step, which have
+ more interesting features in the visualization,
+
+2006-10-04 18:34 tan2
+
+ * examples/Cookbook1/cookbook1.cfg,
+ examples/Cookbook2/cookbook2.cfg,
+ examples/Cookbook3/cookbook3.cfg,
+ examples/Cookbook4/cookbook4.cfg,
+ examples/Cookbook5/cookbook5.cfg,
+ examples/Cookbook6/cookbook6.cfg: * Removed some unnecessary
+ parameters * Changed the layout slightly * Updated the cookbook
+ scripts to be consistent with the manual
+
+2006-10-04 18:32 tan2
+
+ * doc/manual/citcoms.lyx: Updated the Cookbook chapter
+
+2006-10-04 18:24 tan2
+
+ * doc/manual/graphics/cookbook1.jpg, doc/manual/graphics/eq1.eps,
+ doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps,
+ doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps,
+ doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps,
+ doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps,
+ doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps,
+ doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps,
+ doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps,
+ doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps,
+ doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps,
+ doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps,
+ doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps,
+ doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps,
+ doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps,
+ doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps,
+ doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps,
+ doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps,
+ doc/manual/graphics/exp9.eps: Removed unused figures
+
+2006-10-04 01:56 tan2
+
+ * examples/Cookbook6/cookbook6.cfg,
+ examples/Cookbook6/cookbook7.cfg: Renamed file to be consistent
+ with the manual
+
+2006-10-04 01:54 tan2
+
+ * examples/Cookbook6, examples/Cookbook7: Renamed directory to be
+ consistent with the manual
+
+2006-10-02 22:46 tan2
+
+ * examples/Cookbook1/cookbook1.cfg: Using default Rayleigh number,
+ which is stated in the manual. Also updated the comment to be
+ consistent with the manual.
+
+2006-10-02 22:43 tan2
+
+ * doc/manual/citcoms.lyx: Slightly updated postprocessing chapter.
+ Revised Cookbook 1.
+
+2006-09-30 00:56 tan2
+
+ * doc/manual/citcoms.lyx: Updated Chapter 3 "Running CitComS.py"
+ for the .cfg input format, also explained how to launch a
+ parallel job. Some TODO items left.
+
+2006-09-29 23:14 gurnis
+
+ * lib/Full_read_input_from_files.c, lib/Problem_related.c,
+ lib/Regional_lith_age_read_files.c: Fixed age bug in Regional. In
+ Regional_lith_age_read_files.c, find_age_in_MY() was not being
+ converted to a float
+
+2006-09-29 21:50 sue
+
+ * doc/manual/citcoms_cover-layers.pdf,
+ doc/manual/citcoms_cover.pdf: updated version on pdf cover and
+ added pdf layered file
+
+2006-09-28 14:56 luis
+
+ * lib/Output_h5.c, lib/hdf5_related.h: 1. Added a cap dimension for
+ efficient parallel I/O 2. Bulk of data write operations now done
+ in collective mode. 4. Passing various parallel I/O tuning
+ parameters to HDF5 and MPI-IO. 5. Consolidated all data buffers
+ into one (only largest size allocated).
+
+2006-09-28 14:30 luis
+
+ * CitcomS/Components/Output.py, module/setProperties.cc: Fixed typo
+ in names
+
+2006-09-27 23:33 tan2
+
+ * CitcomS/Components/Output.py: * Removed debugging output * Added
+ svn:keywords and svn:mime-type attributes
+
+2006-09-27 20:37 leif
+
+ * setup.py: Relaxed setuptools version requirement to 0.6b1.
+
+2006-09-27 00:24 tan2
+
+ * CitcomS/Components/Output.py, CitcomS/Makefile.am,
+ CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c,
+ lib/Output_h5.c, lib/global_defs.h, lib/output.h,
+ lib/output_h5.h, module/bindings.cc, module/setProperties.cc,
+ module/setProperties.h: * Created new component 'Output.py' for
+ storing output-related properties * Added several input
+ parameters for HDF5 output performance tuning * Moved
+ 'output_format' and 'output_optional' form Solver.py to Output.py
+
+2006-09-26 12:20 luis
+
+ * bin/Makefile.am, examples/Makefile.am, lib/Makefile.am,
+ module/Makefile.am, visual/OpenDXMacro/Makefile.am: Fixed broken
+ 'make dist'
+
+2006-09-26 01:09 leif
+
+ * bin/Makefile.am, bin/pycitcoms.cc, configure.ac, ez_setup.py,
+ module/Exchanger/Makefile.am, module/Makefile.am, setup.py: Made
+ 'Exchanger' optional. Give "--with-exchanger=[yes|no]" as an
+ argument to 'configure' to manually specify whether you want
+ Exchanger; the default is "auto", which means to use Exchanger if
+ it's installed (and on your PYTHONPATH).
+
+ Egg-ified 'configure' checks for Python packages. This means that
+ CitcomS now requires the egg-ified CIG version of Pythia -- and
+ (optionally) the egg-ified Exchanger. Old Pythia/Exchanger
+ installations will not work, as they lack the egg-metadata
+ ('configure' will act as if they are not installed).
+
+ Added 'setup.py', which will automatically download and install
+ the egg version of Pythia -- as well as the egg system itself
+ ('setuptools'). If you want Exchanger, you still must install it
+ manually (the way C++ is used prevents complete egg-ification of
+ Exchanger). Note that 'setup.py' actually checks-out the latest
+ Pythia from the SVN repository. The release version of CitcomS
+ will download a packaged Pythia from the website instead.
+
+2006-09-25 19:13 tan2
+
+ * lib/Output.c, lib/Output_h5.c: Disabled material output, since
+ material control is not working (yet)
+
+2006-09-24 07:28 tan2
+
+ * CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output_h5.c,
+ lib/global_defs.h, module/setProperties.cc: Added new input
+ parameter 'datadir_old' in CitcomS.solver. If output_format=ascii
+ and restart=1, the restart files will be read from
+ ${datadir_old}/${rank}/${datafile_old}.velo.${rank}.${step}. In
+ this case, 'datafile_old' cannot contain '/'. See issue56.
+
+2006-09-22 23:26 tan2
+
+ * CitcomS/Solver/Solver.py, lib/Instructions.c: Write surf and botm
+ output by default (but can be disabled by setting
+ output_optional=''), which is compatible with v2.0.x.
+
+2006-09-22 22:58 tan2
+
+ * lib/Instructions.c: Removed debugging output
+
+2006-09-22 22:29 tan2
+
+ * visual/batchsurf.py: * Fixed issue55 "surf files got deleted by
+ batchsurf.py" * Refactored the codes on machinefile -> nodelist
+
+2006-09-22 22:14 tan2
+
+ * visual/getcoord.sh, visual/getsurf.sh: These scripts accept
+ 'localhost' as a valid machine name now
+
+2006-09-22 22:01 luis
+
+ * lib/Output_h5.c: Bug fix: maxdims[0] is set to H5S_UNLIMITED in
+ extendible datasets, so it should never be incremented.
+
+2006-09-22 20:37 tan2
+
+ * visual/autocombine.py, visual/estimate.py, visual/h5tocap.py,
+ visual/miff2avi, visual/miff2mpg, visual/parser.py,
+ visual/zslice.py: Added 'Id' keyword to the files
+
+2006-09-22 19:19 tan2
+
+ * visual/batchpaste.sh, visual/batchpaste2.sh: Fixed two bugs in
+ post-processing scripts
+
+2006-09-21 23:03 tan2
+
+ * visual/autocombine.py, visual/batchcombine.py,
+ visual/batchpaste.sh, visual/batchpaste2.sh: Updated
+ post-processing script for new output_format options. See
+ issue53.
+
+2006-09-21 21:25 luis
+
+ * lib/Output_h5.c: Allow for optional fields when extending
+ datasets.
+
+2006-09-21 21:17 tan2
+
+ * lib/Output.c, lib/Output_h5.c, lib/Process_buoyancy.c: Refactored
+ out the code computing horizontal average of temperature and rms
+ velocity into a function. This fixes the bug in issue46.
+
+2006-09-21 20:08 tan2
+
+ * lib/Instructions.c: Forgot to change the default value in C
+
+2006-09-21 19:57 tan2
+
+ * CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c,
+ lib/Output_h5.c, lib/global_defs.h: Added new option for
+ "output_format". The current behavior is: * If
+ output_format=="ascii-local" (the default), CitcomS will write
+ ascii files to the directory and prefix specified by "datafile",
+ ie., the same behavior as in v2.0 * If output_format=="ascii",
+ CitcomS will write ascii files to the directory specified by
+ "datadir" with the prefix specified by "datafile". In the case,
+ "datafile" cannot contains the '/' (path seperator) character. *
+ If output_format=="hdf5", CitcomS will write singe HDf5 file to
+ the directory and prefix specified by "datafile".
+
+2006-09-21 17:51 tan2
+
+ * visual/parser.py: Parser will skip lines starting with '[', so
+ that it can parse .cfg file correctly
+
+2006-09-21 17:49 tan2
+
+ * module/setProperties.cc: Removed quotes from output string
+
+2006-09-21 00:18 tan2
+
+ * CitcomS/CoupledApp.py, CitcomS/SimpleApp.py,
+ examples/Cookbook1/cookbook1.cfg,
+ examples/Cookbook2/cookbook2.cfg,
+ examples/Cookbook3/cookbook3.cfg,
+ examples/Cookbook4/cookbook4.cfg,
+ examples/Cookbook5/cookbook5.cfg,
+ examples/Cookbook7/cookbook7.cfg, examples/example0.cfg,
+ examples/example1.cfg: Calculate the needed # of cpu according to
+ mesher properties. There is no longer a need to set
+ launcher.nodes.
+
+2006-09-20 22:51 tan2
+
+ * CitcomS/BaseApplication.py, CitcomS/Solver/CoupledFullSolver.py,
+ CitcomS/Solver/CoupledRegionalSolver.py,
+ CitcomS/Solver/CoupledSolver.py: Added svn:keywprds = Id
+
+2006-09-20 20:47 tan2
+
+ * lib/Output_h5.c: Sync'd h5output_meta() with setProperties
+
+2006-09-20 20:45 tan2
+
+ * CitcomS/Components/IC.py: Fixed the comment
+
+2006-09-20 20:34 tan2
+
+ * CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
+ lib/Advection_diffusion.c, lib/Output_h5.c,
+ module/setProperties.cc: Removed unused parameter 'maxadvtime'
+
+2006-09-20 20:30 tan2
+
+ * CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
+ CitcomS/Components/Const.py, CitcomS/Components/IC.py,
+ CitcomS/Components/Visc.py, module/setProperties.cc: Print out
+ all pyre properties to the pid file
+
+2006-09-20 19:54 tan2
+
+ * lib/Citcom_init.c, lib/Instructions.c, module/mesher.cc,
+ module/setProperties.cc: Saving the input parameters to a unique
+ file 'pidXXXXX.cfg' for archives.
+
+2006-09-19 19:50 luis
+
+ * lib/Output_h5.c: Allocate tensor field buffer only when
+ necessary.
+
+2006-09-19 18:44 tan2
+
+ * citcoms_profile: Since the opendx scripts have the macro path
+ built in the file, there is no need to define $DXMACROS env. var.
+
+2006-09-17 17:32 tan2
+
+ * CitcomS/Solver/Solver.py, examples/Cookbook5/cookbook5.cfg,
+ examples/Full/input.sample, examples/Regional/input.sample,
+ lib/Instructions.c, lib/Output.c, lib/Output_h5.c,
+ lib/global_defs.h, module/setProperties.cc,
+ visual/autocombine.py, visual/batchcombine.py,
+ visual/batchpaste.sh, visual/combine.py,
+ visual/pasteCitcomData.sh: * Added new input parameter 'datadir'
+ in Solver * All outputs are done in 'datadir' directory *
+ Processors write its own ascii output in 'datadir/rank' directory
+ * Post-processing codes and cookbook examples were updated
+ accordingly
+
+2006-09-14 18:14 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.c: added help on usage.
+
+2006-09-13 19:04 maweier
+
+ * visual/Mayavi2/plugins/filter/CitcomSreduce.py: Changed range
+ trait.
+
+2006-09-12 20:50 tan2
+
+ * lib/global_defs.h: Fixed the bug of negative CPU time, which is
+ caused by storing the walltime in insufficient precision
+
+2006-09-11 17:25 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.c: added latest version of file
+ converter in c.
+
+2006-09-11 17:24 maweier
+
+ * visual/Mayavi2/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/Citcoms_VtkDisplay.py,
+ visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
+ visual/Mayavi2/plugins/filter/CitcomSSphere.py,
+ visual/Mayavi2/plugins/filter/CitcomSreduce.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
+ visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
+ Updated licenses.
+
+2006-09-11 17:23 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.c: Update
+
+2006-09-11 00:17 luis
+
+ * visual/Makefile.am, visual/h5steps.c, visual/h5tocap.c: 1. Added
+ utility to extract steps from CitcomS HDF5 file. 2. Changed
+ h5tocombined.c to h5tocap.c in copyright header.
+
+2006-09-11 00:09 luis
+
+ * visual/h5tocap.c: When no frames are specified, print number of
+ available frames.
+
+2006-09-10 09:50 luis
+
+ * visual/Makefile.am, visual/h5tocap.c: 1. Added h5tocap to build
+ procedure 2. Changed h5tocap to read frames from command-line
+ (instead of steps)
+
+2006-09-10 07:36 luis
+
+ * lib/Output_h5.c, visual/estimate.py: Moved connectivity dataset
+ to root group.
+
+2006-09-09 01:45 tan2
+
+ * configure.ac: * set --with-hdf5=auto as default, which will try
+ to detect HDF5 library, if not found, HDF5 support will be
+ disabled * Reported summary at the end of configure
+
+2006-09-09 00:24 tan2
+
+ * configure.ac: Added $PHDF5_HOME env. variables for the home
+ directory of parallel HDF5 lib
+
+2006-09-08 20:59 tan2
+
+ * visual/Makefile.am: Forgot to rename file
+
+2006-09-08 20:27 luis
+
+ * visual/h5tocap.c, visual/h5tocombined.c: Changed name to
+ h5tocap.c
+
+2006-09-08 19:20 tan2
+
+ * visual/h5tocap.py: Added a comment
+
+2006-09-08 19:18 tan2
+
+ * visual/visRegional.cfg: Reverted the accidental check-in at r4498
+
+2006-09-08 19:14 tan2
+
+ * visual/h52combined.py, visual/h5tocap.py, visual/visRegional.cfg:
+ Renamed the conversion script
+
+2006-09-08 19:14 tan2
+
+ * visual/h52combined.py: * Using 'caps' attribute in the input
+ group * frame -> timestep conversion * Cleaned up the code
+
+2006-09-08 15:53 luis
+
+ * lib/Output_h5.c, lib/pytables.h: Removing unnecessary HDF5
+ attribute.
+
+2006-09-08 15:46 luis
+
+ * lib/Output_h5.c: Fix allocation of buffer for connectivity (done
+ per cap, not globally).
+
+2006-09-07 21:07 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.py,
+ visual/Mayavi2/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Fixed connectivity
+ issues. Fixed HdfDisplays wrong status output.
+
+2006-09-06 22:33 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.py,
+ visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Got rid of the
+ iterator to change the order.
+
+2006-09-06 21:01 luis
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.c: Added function to retrieve
+ float attributes from HDF5 file.
+
+2006-09-06 20:18 tan2
+
+ * visual/OpenDXMacro/CitcomSImportHDF5.net.in,
+ visual/OpenDXMacro/Makefile.am: * Made CitcomSImportHDF5 accept
+ NULL (default) input for the caplist * Added CitcomSImportHDF5 to
+ the install list
+
+2006-09-06 19:06 tan2
+
+ * CitcomS/Makefile.am: Forgot backslash (line continuation) after
+ Solver/__init__.py. See issue48.
+
+2006-09-06 18:39 tan2
+
+ * visual/OpenDXMacro/CitcomSImportHDF5.net.in: Added an dx macro to
+ import HDF5 output, this module depends on the Cactus OpenDXutils
+ project (http://www.cactuscode.org/Visualization/openDX)
+
+2006-09-06 16:41 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.c: New C version of the Hdf to Vtk
+ converter.
+
+2006-09-05 22:41 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/README:
+ Bugfixes and a new README on how to use the code.
+
+2006-09-05 21:10 maweier
+
+ * visual/Mayavi2/Citcoms_Hdf2Vtk.py,
+ visual/Mayavi2/Citcoms_hdf2vtk.py: Consistency
+
+2006-09-05 20:53 maweier
+
+ * visual/Mayavi2/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/Citcoms_hdf2vtk.py, visual/Mayavi2/__init__.py,
+ visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
+ visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
+ visual/Mayavi2/plugins/filter/__init__.py: Some minor bugfixes
+
+2006-09-05 20:49 maweier
+
+ * visual/Mayavi2/Citcoms_hdf2vtk.py,
+ visual/Mayavi2/citcoms_hdf2vtk.py: Rename for consistence.
+
+2006-09-02 10:11 luis
+
+ * lib/Instructions.c, lib/Output_h5.c, lib/global_defs.h,
+ visual/estimate.py: Added connectivity datasets (per cap) to HDF5
+ optional output.
+
+2006-09-02 09:31 luis
+
+ * visual/h5tocombined.c: Opened all available cap groups outside
+ the main loop.
+
+2006-08-31 23:06 maweier
+
+ * visual/Mayavi2, visual/Mayavi2/Citcoms_HdfDisplay.py,
+ visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/__init__.py,
+ visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/plugins,
+ visual/Mayavi2/plugins/CitcomHDFThread.py,
+ visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
+ visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
+ visual/Mayavi2/plugins/OpenCitcomSFILES.py,
+ visual/Mayavi2/plugins/__init__.py,
+ visual/Mayavi2/plugins/filter,
+ visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
+ visual/Mayavi2/plugins/filter/CitcomSSphere.py,
+ visual/Mayavi2/plugins/filter/CitcomSreduce.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
+ visual/Mayavi2/plugins/filter/__init__.py,
+ visual/Mayavi2/plugins/plugin_defs,
+ visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
+ New folder structure.
+
+2006-08-31 23:05 maweier
+
+ * visual/Mayavi2: Complete update to new Folder structure.
+
+2006-08-31 14:56 luis
+
+ * visual/h5tocombined.c: Added ability to output multiple timesteps
+ (specified on command-line).
+
+2006-08-31 13:28 luis
+
+ * visual/h5tocombined.c: 1. Cleaned up code in general. 2. Fixed
+ bug in reading coord dataset (need to do it for each cap!).
+
+2006-08-29 23:44 maweier
+
+ * visual/Mayavi2/citcoms_hdf2vtk.py,
+ visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
+ visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowCaps.py: More stable
+ versions. Some performance enhancements.
+
+2006-08-28 23:19 maweier
+
+ * visual/Mayavi2/core/CitcomSHDFUgrid.pyc,
+ visual/Mayavi2/core/__init__.pyc,
+ visual/Mayavi2/filter/CitcomSFilterActions.pyc,
+ visual/Mayavi2/filter/CitcomSSphere.pyc,
+ visual/Mayavi2/filter/CitcomSreduce.pyc,
+ visual/Mayavi2/filter/CitcomSshowCaps.pyc,
+ visual/Mayavi2/filter/__init__.pyc,
+ visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc,
+ visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc,
+ visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc,
+ visual/Mayavi2/plugins/OpenCitcomSFILES.pyc,
+ visual/Mayavi2/plugins/__init__.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSSphere.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSreduce.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc,
+ visual/Mayavi2/plugins/filter/__init__.pyc,
+ visual/Mayavi2/plugins/filter/showcaps.pyc: Deleting Bytecode
+ Files
+
+2006-08-28 23:17 maweier
+
+ * visual/Mayavi2, visual/Mayavi2/HdfDisplay.py,
+ visual/Mayavi2/VtkDisplay.py, visual/Mayavi2/__init__.py,
+ visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/core,
+ visual/Mayavi2/core/CitcomSHDFUgrid.py,
+ visual/Mayavi2/core/CitcomSHDFUgrid.pyc,
+ visual/Mayavi2/core/__init__.py,
+ visual/Mayavi2/core/__init__.pyc, visual/Mayavi2/filter,
+ visual/Mayavi2/filter/CitcomSFilterActions.py,
+ visual/Mayavi2/filter/CitcomSFilterActions.pyc,
+ visual/Mayavi2/filter/CitcomSSphere.py,
+ visual/Mayavi2/filter/CitcomSSphere.pyc,
+ visual/Mayavi2/filter/CitcomSreduce.py,
+ visual/Mayavi2/filter/CitcomSreduce.pyc,
+ visual/Mayavi2/filter/CitcomSshowCaps.py,
+ visual/Mayavi2/filter/CitcomSshowCaps.pyc,
+ visual/Mayavi2/filter/CitcomSshowSurface.py,
+ visual/Mayavi2/filter/__init__.py,
+ visual/Mayavi2/filter/__init__.pyc, visual/Mayavi2/plugins,
+ visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
+ visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc,
+ visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
+ visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc,
+ visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
+ visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc,
+ visual/Mayavi2/plugins/OpenCitcomSFILES.py,
+ visual/Mayavi2/plugins/OpenCitcomSFILES.pyc,
+ visual/Mayavi2/plugins/__init__.py,
+ visual/Mayavi2/plugins/__init__.pyc,
+ visual/Mayavi2/plugins/filter,
+ visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
+ visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSSphere.py,
+ visual/Mayavi2/plugins/filter/CitcomSSphere.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSreduce.py,
+ visual/Mayavi2/plugins/filter/CitcomSreduce.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
+ visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc,
+ visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
+ visual/Mayavi2/plugins/filter/__init__.py,
+ visual/Mayavi2/plugins/filter/__init__.pyc,
+ visual/Mayavi2/plugins/filter/showcaps.pyc,
+ visual/Mayavi2/plugins/plugin_defs,
+ visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
+ Files for Mayavi2 plugins
+
+2006-08-28 21:20 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: fixed man
+ cover, removed pg no., fixed date, added table of figures,
+ enabled URL hotlinks
+
+2006-08-26 00:49 tan2
+
+ * lib/Full_boundary_conditions.c, lib/Full_parallel_related.c,
+ lib/Full_version_dependent.c, lib/Phase_change.c,
+ lib/Process_buoyancy.c, lib/Regional_boundary_conditions.c,
+ lib/Regional_parallel_related.c,
+ lib/Regional_version_dependent.c, lib/Size_does_matter.c,
+ lib/Viscosity_structures.c: Flushed debugging output
+
+2006-08-25 23:15 tan2
+
+ * doc/manual/citcoms.lyx: Improved the section of full CitcomS
+ visualization. Fixed issue44
+
+2006-08-24 23:46 luis
+
+ * visual/estimate.py: Added script to estimate the size of the
+ output from CitcomS.
+
+2006-08-24 20:08 tan2
+
+ * CitcomS/CoupledApp.py, CitcomS/Layout.py: Renamed some attributes
+
+2006-08-24 20:08 tan2
+
+ * CitcomS/Makefile.am: Updated file list
+
+2006-08-24 19:40 tan2
+
+ * CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
+ CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/__init__.py:
+ Changed the class names
+
+2006-08-24 19:34 tan2
+
+ * CitcomS/Coupler/CoarseGridExchanger.py,
+ CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
+ CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/Exchanger.py,
+ CitcomS/Coupler/FineGridExchanger.py: Renamed *Exchanger.py to
+ *Coupler.py
+
+2006-08-24 19:31 tan2
+
+ * CitcomS/Components/Exchanger, CitcomS/Coupler,
+ CitcomS/Coupler.py: Started refactoring Coupler and Exchanger ...
+
+2006-08-24 19:27 tan2
+
+ * CitcomS/BaseApplication.py, CitcomS/CoupledApp.py,
+ CitcomS/SimpleApp.py, CitcomS/Solver/CoupledFullSolver.py,
+ CitcomS/Solver/CoupledRegionalSolver.py,
+ CitcomS/Solver/CoupledSolver.py, CitcomS/Solver/Solver.py,
+ CitcomS/Solver/__init__.py, bin/Makefile.am, bin/citcoms.in,
+ bin/coupledcitcoms.in: * Refactored coupler-related codes from
+ Solver.py to CoupledSolver.py * Created CoupledFullSolver.py and
+ CoupledRegionalSolver.py * Refactored common codes between
+ CoupledApp.py and SimpleApp.py to BaseApplication.py * Changed
+ the facility names in CoupledApp.py * Created a coupledcitcoms
+ script
+
+2006-08-24 02:47 luis
+
+ * lib/Output_h5.c, lib/hdf5_related.h: Added /cap/average/coord
+ dataset
+
+2006-08-23 23:24 luis
+
+ * lib/Output_h5.c: Fixed silly typos.
+
+2006-08-23 23:16 luis
+
+ * lib/Output_h5.c, lib/hdf5_related.h: 1. Grouped horizontal
+ average data into its own HDF5 group. 2. All datasets are
+ referenced using relative paths (to its own cap group).
+
+2006-08-22 18:24 luis
+
+ * lib/Output_h5.c, lib/hdf5_related.h: Data buffer in field_t
+ struct should be a float.
+
+2006-08-22 13:08 luis
+
+ * lib/Output_h5.c: 1. Fixed PyTables attributes for time dataset
+ (bugfix) 2. Added surf and botm data (optional output) 3. Added
+ horizontal averages (optional output)
+
+2006-08-21 22:42 tan2
+
+ * lib/Output_h5.c: Added two attributes to /input group * 'scalev'
+ : velocity scale, in cm/yr * 'scalet' : time scale, in Myrs
+
+2006-08-21 21:38 luis
+
+ * visual/h5tocombined.c: Added program to convert the HDF5 output
+ file to the ASCII combined file, using the HDF5 C-API.
+
+2006-08-18 18:43 tan2
+
+ * bin/Citcom.c, lib/Output.c, lib/Output_h5.c, lib/output.h,
+ lib/output_h5.h, module/outputs.cc: Refactored and Merged
+ output_pseudo_surf with output
+
+2006-08-18 04:59 tan2
+
+ * CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Instructions.c,
+ lib/Output.c, lib/Output_h5.c, lib/global_defs.h,
+ module/outputs.cc, module/setProperties.cc: * Closed E->fp_out
+ properly * Fixed a bug when output_format is illegal * Added new
+ input parameter "output_optional", which is a comma seperated
+ list of fields to output. Currently, supported outputs are
+ "pressure", "stress", "surf", "botm", and "average". * Changed
+ the format of stress output to be consistent with other output
+
+2006-08-15 21:50 sue
+
+ * doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf,
+ doc/manual/citcoms_cover2-0-2.pdf: deleted versioned files
+
+2006-08-15 20:48 tan2
+
+ * lib/Citcom_init.c, lib/Instructions.c: Added 'output_format'
+ input for stand-alone version
+
+2006-08-15 20:46 tan2
+
+ * lib/global_defs.h: Commented out an unused include file
+
+2006-08-15 20:14 sue
+
+ * doc/manual/citcoms.lyx: one more cross-reference fix
+
+2006-08-15 19:46 sue
+
+ * doc/manual/citcoms.lyx: fixed tan's requests and recoded tables
+ to use space better
+
+2006-08-15 18:43 tan2
+
+ * doc/manual/citcoms.lyx: Fixed various typos/inconsistency/errors
+ Added some comments (started with 'tan2:')
+
+2006-08-15 14:02 luis
+
+ * lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Fixed issues
+ with time dataset.
+
+2006-08-15 12:09 luis
+
+ * lib/Output_h5.c, lib/hdf5_related.h: 1. Introduced field_t
+ object, and updated the appropriate functions to use it. 2.
+ Changed to independent parallel I/O for dataset writes. 3. Using
+ collective calls to extend time-varying datasets (bugfix).
+
+2006-08-15 06:26 tan2
+
+ * doc/manual/citcoms.lyx: Updated the status of multi-grid solver
+
+2006-08-14 22:24 sue
+
+ * doc/manual/citcoms.lyx: restored 2-sided page setting
+
+2006-08-14 19:52 sue
+
+ * doc/manual/citcoms.lyx: got appendices into toc
+
+2006-08-14 19:29 sue
+
+ * doc/manual/citcoms.lyx: changed margins and doc settings as
+ requested
+
+2006-08-14 11:52 luis
+
+ * lib/Output_h5.c: 1. Switching default data transfer property to
+ use independent parallel I/O. 2. Time-varying fields are now
+ created without an extent along time-dimension. 3. Consolidated
+ some debug statements into a single printf.
+
+2006-08-14 11:22 luis
+
+ * lib/Output_h5.c, lib/hdf5_related.h: Added step column to the
+ /time table dataset.
+
+2006-08-14 11:01 luis
+
+ * lib/Output_h5.c: Determine hyperslab block size based on mpi
+ process coordinates, not mpi process rank (bugfix).
+
+2006-08-14 08:38 luis
+
+ * lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Added some
+ useful set_attribute*() functions.
+
+2006-08-12 22:47 gurnis
+
+ * lib/Full_boundary_conditions.c, lib/Lith_age.c: Fix bug
+ associated with assimilating age grids in global models. Only
+ relevant change was made in the subroutine
+ full_temperature_boundary_condition() in which I now make a call
+ to lith_age_temperature_bound_adj() if lith_age_time is on.
+
+2006-08-12 02:37 luis
+
+ * visual/h52combined.py: Rearranged (i,j,k) indices for
+ consistency, i.e. to correspond to (x,y,z) coords instead of
+ (y,x,z). Also, moved constant format string outside of the loop
+ body.
+
+2006-08-11 21:36 tan2
+
+ * doc/manual/citcoms.lyx: Fixed the status of CitcomS.py on
+ TeraGrid
+
+2006-08-11 20:28 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: added
+ leif's gnu build sys additions
+
+2006-08-11 20:05 sue
+
+ * doc/manual/citcoms.lyx: incorporated tan2 changes/comments
+
+2006-08-11 06:11 leif
+
+ * visual/Makefile.am: Whoops -- macro references from visual/*.net
+ must refer to subdirectory 'OpenDXMacro'.
+
+2006-08-11 01:55 leif
+
+ * bin/Makefile.am, bin/citcoms.in, configure.ac,
+ visual/Makefile.am, visual/OpenDXMacro,
+ visual/OpenDXMacro/Makefile.am: Build OpenDX macros in-place
+ during 'make'. Remove 'citcoms' script during 'uninstall'. Also,
+ partial fixes for MPICH2... one still needs to add
+ -DMPICH_SKIP_MPICXX to CPPFLAGS, however; see issue14.
+
+2006-08-10 20:48 sue
+
+ * doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf,
+ doc/manual/citcoms_cover2-0-2.pdf: added 2.0.2 manual draft and
+ cover
+
+2006-08-08 21:24 tan2
+
+ * lib/Output_h5.c, lib/PyTables.c: Made the code compile when
+ configured --with-hdf5=no
+
+2006-08-08 20:47 luis
+
+ * configure.ac: Fix checks for hdf5.h and for parallel HDF5. Should
+ now be performed only if --with-hdf5 is specified.
+
+2006-08-08 04:55 ces74
+
+ * examples/Cookbook7/cookbook7.cfg: * fixed a bug in the module
+ specification: - vsolver --> solver.vsolver - tsolver -->
+ solver.tsolver.
+
+2006-08-07 21:24 luis
+
+ * lib/Output_h5.c, lib/hdf5_related.h: Added time dataset
+
+2006-08-07 06:47 luis
+
+ * configure.ac: Added configure check for Parallel-HDF5
+
+2006-08-07 06:38 luis
+
+ * lib/Makefile.am: Removed reference to nonexistent directory
+
+2006-08-07 06:10 luis
+
+ * bin/Makefile.am, configure.ac, lib/Citcom_init.c,
+ lib/Makefile.am, lib/hdf5_related.h, module/Makefile.am: Changed
+ configure script to compile everything with -DUSE_HDF5 when HDF5
+ support is enabled (--with-hdf5)
+
+2006-08-07 04:56 luis
+
+ * lib/Makefile.am, lib/global_defs.h, lib/hdf5_info.h,
+ lib/hdf5_related.h: Need to maintain multiple structs in header
+ file, so renaming hdf5_info.h to hdf5_related.h
+
+2006-08-07 00:46 luis
+
+ * lib/Output_h5.c: Commented out debug statements
+
+2006-08-05 12:48 luis
+
+ * lib/Output_h5.c: Added h5output_meta(), and saved to the HDF5
+ input group the same input parameters that are used in
+ pyCitcom_*_set_properties().
+
+2006-08-05 12:43 luis
+
+ * lib/PyTables.c, lib/pytables.h: Added set_attribute_numerical*()
+ functions for creating numerical attributes (int, float, double,
+ ...) on a specified HDF5 object.
+
+2006-08-05 00:26 tan2
+
+ * visual/Makefile.am: Added h52combined.py to the install list
+
+2006-08-05 00:14 tan2
+
+ * visual/h52combined.py: Added a script to convert the HDF5 output
+ file to the ASCII combined file, using PyTables extension
+ package.
+
+2006-08-04 23:37 tan2
+
+ * lib/Advection_diffusion.c: Added some comments for filter()
+
+2006-08-04 23:20 luis
+
+ * lib/Output_h5.c: Output viscosity.
+
+2006-08-04 23:13 luis
+
+ * lib/Output_h5.c, lib/hdf5_info.h: Renamed E->hdf5.step to
+ something less confusing: E->hdf5.count
+
+2006-08-04 21:46 tan2
+
+ * CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Output.c,
+ lib/output.h, module/bindings.cc, module/outputs.cc,
+ module/outputs.h: * Fixed skipped time output when
+ monitoringFrequency > 1, which was introduced in r4118 * Forgot
+ to change to the E->output function pointer in r4126
+
+2006-08-03 14:14 luis
+
+ * lib/Output_h5.c: Changed h5output() so that it prints an error if
+ the C macro USE_HDF5 is not defined (and similarly for
+ h5output_pseudo_surf())
+
+2006-08-03 14:03 luis
+
+ * lib/Output_h5.c, lib/hdf5_info.h: Fix bug in behavior for values
+ of monitoringFrequency > 1 by keeping an internal count of steps
+ (Python does not pass monitoringFrequency to C code).
+
+2006-08-03 11:17 luis
+
+ * module/PyxMPI/PyxMPI.c: Regenerated PyxMPI.c with Pyrex 0.9.4 to
+ fix GCC4 lvalue-casting error.
+
+2006-08-03 11:14 luis
+
+ * configure.ac: Fixed typo in configure.ac and added conditional
+ check for hdf5.h header.
+
+2006-08-03 04:22 luis
+
+ * lib/Output_h5.c: 1. Disabled creation of surf & botm (temporary)
+ 2. Only outputs (per cap) are currently coord, velocity &
+ temperature fields 3. For clarity, added indentation to the
+ debugging output
+
+2006-08-03 03:05 luis
+
+ * lib/Output_h5.c: Rewrote h5write_field().
+
+2006-08-03 02:31 luis
+
+ * lib/Output_h5.c: Renamed h5write_array_hyperslab() to
+ h5write_dataset() and fixed the comment describing the usage of
+ h5create_field().
+
+2006-08-03 02:15 luis
+
+ * lib/Output_h5.c: Rewrote h5create_field() to use indices instead
+ of if-else branches when building the arguments (dims, maxdims,
+ chunkdims) for dataset creation.
+
+2006-08-03 01:43 luis
+
+ * lib/Output_h5.c: In h5create_dataset(), renamed local variable
+ filespace into dataspace.
+
+2006-08-03 01:42 luis
+
+ * lib/Output_h5.c: Renamed h5create_array() to h5create_dataset()
+ and made sure that the datasets created by that function are
+ compatibles with PyTables.
+
+2006-08-03 01:30 luis
+
+ * lib/Output_h5.c: Updated debug statements.
+
+2006-08-03 01:05 luis
+
+ * lib/Output_h5.c: Added h5create_file() and modified
+ h5create_group() so that the files and groups created with these
+ functions are compatible with PyTables.
+
+2006-08-03 01:04 luis
+
+ * lib/Makefile.am, lib/PyTables.c: Fixed typo in PyTables.c and
+ added it to the sources in Makefile.am
+
+2006-08-02 23:38 sue
+
+ * doc/manual/citcoms.lyx: added cover image
+
+2006-08-02 19:42 sue
+
+ * doc/manual/citcoms.lyx, doc/manual/citcoms_book.xml,
+ doc/manual/graphics.tar.gz: replace manual with lyx manual
+
+2006-08-02 00:17 tan2
+
+ * lib/Instructions.c, lib/Output_h5.c: Open and close HDF5 output
+ properly
+
+2006-08-01 23:25 luis
+
+ * lib/Output_h5.c: Added debug statements.
+
+2006-08-01 23:17 luis
+
+ * lib/pytables.h: Updated prototypes for the pytables-derived
+ functions.
+
+2006-08-01 23:09 luis
+
+ * lib/global_defs.h: Added flags to control which data
+ (viscosity,stress,pressure) gets written to output.
+
+2006-08-01 22:50 luis
+
+ * lib/hdf5_info.h: Consolidated buffers by size instead of by type.
+
+2006-08-01 22:47 luis
+
+ * lib/PyTables.c: Use strings as default HDF5 attribute type.
+
+2006-08-01 19:21 tan2
+
+ * CitcomS/Solver/Solver.py, module/bindings.cc, module/outputs.cc,
+ module/outputs.h: Closing output files in Solver.py
+
+2006-08-01 19:06 tan2
+
+ * CitcomS/Components/Param.py, CitcomS/Solver/Solver.py,
+ module/setProperties.cc: Moved the 'output_format' property from
+ Param.py to Solver.py
+
+2006-08-01 05:57 tan2
+
+ * CitcomS/Components/Param.py, module/outputs.cc,
+ module/setProperties.cc: * Created pyre property for
+ 'output_format' * Changed the output function pointer in the
+ python binding
+
+2006-08-01 00:54 luis
+
+ * bin/Makefile.am, configure.ac, lib/Makefile.am: Added --with-hdf5
+ options to configure.ac. Also, modified Makefile.am so that
+ Output_h5.o is compiled.
+
+2006-08-01 00:23 tan2
+
+ * CitcomS/Controller.py, CitcomS/Solver/Solver.py,
+ module/bindings.cc, module/misc.cc, module/misc.h: Completely
+ fixed issue35 (inconsistent times) and related problems * t, dt,
+ step are modified only in the C code. Their python counterparts
+ are read-only * Changed the ancestor of the Controller from
+ Pyre's SimulationController to Pyre's Component, as the
+ SimulationController hinders the use of read-only properties *
+ Changed the ancestor of the Solver from Pyre's Solver to Pyre's
+ Component, as Pyre's Solver hinders the use of read-only
+ properties
+
+2006-07-31 23:07 tan2
+
+ * lib/Instructions.c: Changed the default value of 'layerd' from
+ 2800 km (the depth of the mantle) to 6371 km (the radius of the
+ Earth), which is necessary to dimensionalize the time
+
+2006-07-31 23:04 tan2
+
+ * bin/Citcom.c, lib/Instructions.c, lib/global_defs.h,
+ module/mesher.cc: Added logic to switch the E->output function
+ pointer
+
+2006-07-29 00:08 luis
+
+ * lib/Output_h5.c: Added two methods for writing to HDF5 arrays
+ (refactored from CitcomCU).
+
+2006-07-28 22:12 luis
+
+ * lib/Output_h5.c: Fixed typos in h5output_coord()
+
+2006-07-28 22:06 tan2
+
+ * CitcomS/Solver/Solver.py: Removed unused variables due to
+ refactoring of time output
+
+2006-07-28 18:37 tan2
+
+ * lib/Output.c: Flushed the E->fptime stream after each output
+
+2006-07-28 18:36 tan2
+
+ * lib/Instructions.c: Added missing function declaration
+
+2006-07-27 22:02 tan2
+
+ * CitcomS/Controller.py, CitcomS/Solver/Solver.py, bin/Citcom.c,
+ lib/Instructions.c, lib/Output.c, lib/global_defs.h,
+ module/mesher.cc: Moved the responsibility of time output from
+ Citcom.c and Solver.py to Output.c, which includes the following
+ changes * open .time file at either mesher.cc (for pyre run) or
+ Instructions.c (for C run) * .time file is opened and closed only
+ by the rank-0 processor. This will avoid multiple processors
+ opening/writing/closing on the same file. Similar modification is
+ necessary for the .log file. * created two variables
+ E->monitor.cpu_time_at_start and
+ E->monitor.cpu_time_at_last_cycles for storing the wall clock
+ time at startup and last timestep, respectively * output .time
+ file in output_time() in Output.c
+
+2006-07-27 21:06 luis
+
+ * lib/Output_h5.c: Refactored code for array creation.
+
+2006-07-27 21:04 luis
+
+ * lib/hdf5_info.h: Eliminated unecessary buffer arrays.
+
+2006-07-27 19:57 tan2
+
+ * examples/example0.cfg: forgot to change the 'datafile' parameter
+
+2006-07-24 11:22 luis
+
+ * lib/Output_h5.c: Prepare output functions for optional HDF5
+ configuration with autoconf.
+
+2006-07-24 11:18 luis
+
+ * lib/global_defs.h: Added output function pointer to All_variables
+ struct.
+
+2006-07-19 20:19 tan2
+
+ * examples/example0.cfg: example script of single-processor run
+
+2006-07-19 18:42 luis
+
+ * lib/global_defs.h, lib/hdf5_info.h: Created new hdf5 struct
+ member within the All_variables struct.
+
+2006-07-18 23:42 sue
+
+ * doc/manual/graphics, doc/manual/graphics/c_fig1.eps,
+ doc/manual/graphics/c_fig10.eps, doc/manual/graphics/c_fig2.eps,
+ doc/manual/graphics/c_fig3.jpg, doc/manual/graphics/c_fig4.eps,
+ doc/manual/graphics/c_fig5.eps, doc/manual/graphics/c_fig6.jpg,
+ doc/manual/graphics/c_fig7.eps, doc/manual/graphics/c_fig8.eps,
+ doc/manual/graphics/c_fig9.eps,
+ doc/manual/graphics/cookbook1.2.jpg,
+ doc/manual/graphics/cookbook1.eps,
+ doc/manual/graphics/cookbook1.jpg,
+ doc/manual/graphics/cookbook1.png,
+ doc/manual/graphics/cookbook2.2.eps,
+ doc/manual/graphics/cookbook2.2eps,
+ doc/manual/graphics/cookbook2.eps,
+ doc/manual/graphics/cookbook3.eps,
+ doc/manual/graphics/cookbook4.eps,
+ doc/manual/graphics/cookbook5.2.eps,
+ doc/manual/graphics/cookbook5.eps,
+ doc/manual/graphics/cookbook6.2.eps,
+ doc/manual/graphics/cookbook6.eps,
+ doc/manual/graphics/cookbook7.eps, doc/manual/graphics/eq1.eps,
+ doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps,
+ doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps,
+ doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps,
+ doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps,
+ doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps,
+ doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps,
+ doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps,
+ doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps,
+ doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps,
+ doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps,
+ doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps,
+ doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps,
+ doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps,
+ doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps,
+ doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps,
+ doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps,
+ doc/manual/graphics/exp9.eps: adding graphics directory
+
+2006-07-18 23:05 sue
+
+ * doc/manual/citcoms_book.xml: updated dtd address
+
+2006-07-18 01:00 luis
+
+ * lib/PyTables.c, lib/pytables.h: Provide an API for creating
+ PyTables-compatible HDF5 files.
+
+2006-07-17 23:31 luis
+
+ * lib/Output_h5.c, lib/output_h5.h: For the new HDF5 output format,
+ use a similar API as in Output.c Copying the bodies from the old
+ functions for now, but prefixing the function name with 'h5'.
+
+2006-07-15 02:14 leif
+
+ * CitcomS/SimpleApp.py: Bug fix in
+ _getPrivateDepositoryLocations(); updated usage().
+
+2006-07-13 23:41 leif
+
+ * examples/Cookbook1/cookbook1.cfg,
+ examples/Cookbook1/cookbook1.sh,
+ examples/Cookbook2/cookbook2.cfg,
+ examples/Cookbook2/cookbook2.sh,
+ examples/Cookbook3/cookbook3.cfg,
+ examples/Cookbook3/cookbook3.sh,
+ examples/Cookbook4/cookbook4.cfg,
+ examples/Cookbook4/cookbook4.sh,
+ examples/Cookbook5/cookbook5.cfg,
+ examples/Cookbook5/cookbook5.sh,
+ examples/Cookbook7/cookbook7.cfg,
+ examples/Cookbook7/cookbook7.sh, examples/example1.sh,
+ tests/Makefile.am, tests/citcomsfull.sh.in,
+ tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Nuked
+ citcoms{full,regional}.sh, coupledcitcoms.sh. Converted cookbook
+ *.sh files to *.cfg files, and sprinkled-in some comments derived
+ from the manual.
+
+2006-07-13 20:06 leif
+
+ * configure.ac: Fix for broken "make install" on Pangu (discovered
+ by Lydia): add both 'pythondir' and 'pyexecdir' to
+ PYTHONPATH/sys.path.
+
+2006-07-07 23:54 leif
+
+ * bin/pycitcoms.cc: Temporary work-around for broken _mpimodule on
+ Pangu.
+
+2006-07-07 23:07 tan2
+
+ * CitcomS/Controller.py: Renamed extension module (see r3983)
+
+2006-07-07 22:35 leif
+
+ * CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
+ CitcomS/Components/BC.py, CitcomS/Components/Const.py,
+ CitcomS/Components/Exchanger/Exchanger.py,
+ CitcomS/Components/Exchanger/Inlet.py,
+ CitcomS/Components/Exchanger/Outlet.py, CitcomS/Components/IC.py,
+ CitcomS/Components/Param.py, CitcomS/Components/Phase.py,
+ CitcomS/Components/Sphere/FullSphere.py,
+ CitcomS/Components/Sphere/RegionalSphere.py,
+ CitcomS/Components/Sphere/Sphere.py,
+ CitcomS/Components/Stokes_solver/Incompressible.py,
+ CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py,
+ CitcomS/Makefile.am, CitcomS/SimpleApp.py,
+ CitcomS/Solver/FullSolver.py, CitcomS/Solver/RegionalSolver.py,
+ CitcomS/Solver/Solver.py, bin/Makefile.am, bin/citcoms.in,
+ bin/pycitcoms.cc, module/CitcomSmodule.cc,
+ module/CitcomSmodule.h, module/Exchanger/Exchangermodule.cc,
+ module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am,
+ module/Full, module/Makefile.am, module/Regional,
+ module/Regionalmodule.cc, module/advdiffu.cc, module/advdiffu.h,
+ module/bindings.cc, module/bindings.h, module/exceptions.cc,
+ module/exceptions.h, module/initial_conditions.cc,
+ module/initial_conditions.h, module/mesher.cc, module/mesher.h,
+ module/misc.cc, module/misc.h, module/outputs.cc,
+ module/outputs.h, module/setProperties.cc,
+ module/setProperties.h, module/stokes_solver.cc,
+ module/stokes_solver.h, tests/exchange.py: Moved & renamed
+ extension modules:
+
+ CitcomS.CitcomS -> CitcomsLib CitcomS.Exchanger -> ExchangerLib
+
+ Top-level modules allow easy toggling between embedding &
+ extending without any special hacks in the embedding case. Also,
+ it allows the Python scripts to be installed under 'libdir'
+ instead of 'libexecdir', although this is a minor issue.
+
+ Also: moved module/Regional/* source to module/* to really
+ complete the Full/Regional merge (there is only one CitcomS
+ extension module now). Plus, a bug fix in collectUserInput.
+
+2006-07-07 21:36 tan2
+
+ * CitcomS/Controller.py, CitcomS/Solver/Solver.py,
+ module/Regional/bindings.cc, module/Regional/misc.cc,
+ module/Regional/misc.h: A quick fix to issue35 "inconsistent
+ times in C and Pyre"
+
+2006-07-07 00:54 leif
+
+ * bin/Makefile.am, configure.ac, lib/Advection_diffusion.c,
+ lib/BC_util.c, lib/Citcom_init.c, lib/Common,
+ lib/Construct_arrays.c, lib/Convection.c, lib/Drive_solvers.c,
+ lib/Element_calculations.c, lib/Full,
+ lib/Full_boundary_conditions.c, lib/Full_geometry_cartesian.c,
+ lib/Full_lith_age_read_files.c, lib/Full_obsolete.c,
+ lib/Full_parallel_related.c, lib/Full_read_input_from_files.c,
+ lib/Full_solver.c, lib/Full_sphere_related.c,
+ lib/Full_version_dependent.c, lib/General_matrix_functions.c,
+ lib/Global_operations.c, lib/Initial_temperature.c,
+ lib/Instructions.c, lib/Interuption.c, lib/Lith_age.c,
+ lib/Makefile.am, lib/Nodal_mesh.c, lib/Obsolete.c, lib/Output.c,
+ lib/Pan_problem_misc_functions.c, lib/Parallel_util.c,
+ lib/Parsing.c, lib/Phase_change.c, lib/Problem_related.c,
+ lib/Process_buoyancy.c, lib/Regional,
+ lib/Regional_boundary_conditions.c,
+ lib/Regional_geometry_cartesian.c,
+ lib/Regional_lith_age_read_files.c, lib/Regional_obsolete.c,
+ lib/Regional_parallel_related.c,
+ lib/Regional_read_input_from_files.c, lib/Regional_solver.c,
+ lib/Regional_sphere_related.c, lib/Regional_version_dependent.c,
+ lib/Shape_functions.c, lib/Size_does_matter.c,
+ lib/Solver_conj_grad.c, lib/Solver_multigrid.c,
+ lib/Sphere_harmonics.c, lib/Sphere_util.c,
+ lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c,
+ lib/Tracer_advection.c, lib/Viscosity_structures.c,
+ lib/advection.h, lib/advection_diffusion.h, lib/citcom_init.h,
+ lib/convection_variables.h, lib/drive_solvers.h,
+ lib/element_definitions.h, lib/global_defs.h,
+ lib/initial_temperature.h, lib/interuption.h, lib/lith_age.h,
+ lib/output.h, lib/parallel_related.h, lib/parsing.h,
+ lib/phase_change.h, lib/solver.h, lib/sphere_communication.h,
+ lib/temperature_descriptions.h, lib/tracer_defs.h,
+ lib/viscosity_descriptions.h, module/Exchanger/Makefile.am,
+ module/Makefile.am: Avoid shared libraries altogether when
+ embedding. Shared libs are very likely to fail with static
+ MPICH... this was confirmed when the link failed on Eh's iBook.
+
+ Also completed the Full/Regional merge by flatting the directory
+ structure under 'lib'.
+
+2006-07-06 23:20 leif
+
+ * CitcomS, CitcomS/Components,
+ CitcomS/Components/Advection_diffusion,
+ CitcomS/Components/Exchanger, CitcomS/Components/Sphere,
+ CitcomS/Components/Stokes_solver, CitcomS/Makefile.am,
+ CitcomS/SimpleApp.py, CitcomS/Solver, CitcomS/__init__.py,
+ CitcomS/__init__.py.in, Makefile.am, bin/Makefile.am,
+ configure.ac: Issue32: "make install" is now optional. Users can
+ now simply "configure", "make", and then add the "bin"
+ subdirectory of the source/build directory to their PATH.
+
+ In this mode, changes to C/C++ simply require a "make" from the
+ top-level directory ("make" from a subdirectory will not work in
+ the near future). Changes to the Python code do not require you
+ to run "make" at all -- simply re-run 'citcoms'.
+
+2006-07-06 22:22 leif
+
+ * CitcomS, bin, drivers, pyre: Renamed directories in preparation
+ for next check-in:
+
+ pyre -> CitcomS drivers -> bin
+
+ This is to work-around this error message from 'svn':
+
+ "new node revision ID without delete".
+
+ I am not loving Subversion right now. Wasn't the whole point that
+ it handles renames gracefully?
+
+2006-07-06 18:16 leif
+
+ * Make.mm, drivers/Full, drivers/Make.mm, drivers/Regional,
+ drivers/local.def, etc/Make.mm, lib/Common/Make.mm,
+ lib/Common/local.def, lib/Full/Make.mm, lib/Full/local.def,
+ lib/Make.mm, lib/Regional/Make.mm, lib/Regional/local.def,
+ lib/local.def, local.def, module/Exchanger/Make.mm,
+ module/Full/Make.mm, module/Full/local.def, module/Make.mm,
+ module/Regional/Make.mm, module/Regional/local.def,
+ pyre/Components/Advection_diffusion/Make.mm,
+ pyre/Components/Exchanger/Make.mm, pyre/Components/Make.mm,
+ pyre/Components/Sphere/Make.mm,
+ pyre/Components/Stokes_solver/Make.mm, pyre/Make.mm,
+ pyre/Solver/Make.mm, pyre/local.def, tests/Make.mm,
+ tests/local.def, visual/Make.mm: Nuked "Make.mm" files, which are
+ no longer used.
+
+2006-07-06 02:53 leif
+
+ * examples/example1.cfg, pyre/Components/CodecConfig.py,
+ pyre/Components/HackedConfigParser.py, pyre/Makefile.am,
+ pyre/SimpleApp.py: Added the ability to use ".cfg" files instead
+ of clumsy shell scripts for specifying parameters.
+
+ Example usage:
+
+ citcoms example1.cfg
+
+ (The file 'example1.cfg' is checked-in under 'examples'.)
+
+ The code which made this possible was copied & pasted from
+ Specfem project; it will be factored-out into a shared package at
+ some point...
+
+2006-07-06 02:16 leif
+
+ * Makefile.am, configure.ac, drivers/Citcom.c, drivers/Makefile.am,
+ drivers/citcoms.in, drivers/pycitcoms.cc, etc/CitcomS.pml.in,
+ etc/Makefile.am, lib/Common/Advection_diffusion.c,
+ lib/Common/BC_util.c, lib/Common/Construct_arrays.c,
+ lib/Common/Convection.c, lib/Common/Element_calculations.c,
+ lib/Common/General_matrix_functions.c,
+ lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
+ lib/Common/Lith_age.c, lib/Common/Makefile.am,
+ lib/Common/Nodal_mesh.c, lib/Common/Parallel_util.c,
+ lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
+ lib/Common/Size_does_matter.c, lib/Common/Solver_multigrid.c,
+ lib/Common/Sphere_util.c, lib/Common/global_defs.h,
+ lib/Common/lith_age.h, lib/Common/parallel_related.h,
+ lib/Common/solver.h, lib/Full/Boundary_conditions.c,
+ lib/Full/Geometry_cartesian.c, lib/Full/Lith_age.c,
+ lib/Full/Lith_age_read_files.c, lib/Full/Makefile.am,
+ lib/Full/Parallel_related.c, lib/Full/Read_input_from_files.c,
+ lib/Full/Solver.c, lib/Full/Sphere_related.c,
+ lib/Full/Version_dependent.c, lib/Makefile.am,
+ lib/Regional/Boundary_conditions.c,
+ lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c,
+ lib/Regional/Lith_age_read_files.c, lib/Regional/Makefile.am,
+ lib/Regional/Parallel_related.c,
+ lib/Regional/Read_input_from_files.c, lib/Regional/Solver.c,
+ lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
+ module/CitcomSmodule.cc, module/CitcomSmodule.h,
+ module/Exchanger/Exchangermodule.cc,
+ module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am,
+ module/Full/Makefile.am, module/Makefile.am, module/PyxMPI,
+ module/PyxMPI/PyxMPI.c, module/PyxMPI/PyxMPI.pyx,
+ module/PyxMPI/cmpi.pxd, module/Regional/Makefile.am,
+ module/Regional/bindings.cc, module/Regional/mesher.cc,
+ module/Regional/misc.cc, module/Regional/misc.h,
+ pyre/Components/Advection_diffusion/Advection_diffusion.py,
+ pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
+ pyre/Components/Const.py, pyre/Components/IC.py,
+ pyre/Components/Launchers.py, pyre/Components/Param.py,
+ pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py,
+ pyre/Components/Sphere/RegionalSphere.py,
+ pyre/Components/Sphere/Sphere.py,
+ pyre/Components/Stokes_solver/Incompressible.py,
+ pyre/Components/Tracer.py, pyre/Components/Visc.py,
+ pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
+ pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
+ tests/Makefile.am, tests/citcomsfull.sh.in,
+ tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Added
+ the capability to embed Python instead of extending it. This
+ creates one, big monolithic executable, 'pycitcoms', which
+ contains all CitcomS code and an embedded Python interpreter.
+ Embedding works-around MPI portability issues. (See issue15 for
+ details.) Embed by default.
+
+ Configure with '--disable-embedding' to build the old way with
+ ".so" extension modules. This is *NOT* guaranteed to work unless
+ you have a shared MPI library. The ugly hacks which made it work
+ in the past (even with a static "libmpich.a", for example) are no
+ longer supported.
+
+ Merged "Full" and "Regional" into a single library to cut down on
+ redundancy, both in the source code and in the amount of object
+ code which is produced. (I performed this merge so that I would
+ only need a single 'pycitcoms' intepreter, instead of two.)
+
+2006-06-12 17:43 gurnis
+
+ * lib/Common/Advection_diffusion.c,
+ lib/Common/Initial_temperature.c, lib/Common/Problem_related.c,
+ lib/Full/Read_input_from_files.c, pyre/Solver/Solver.py: Fixed
+ restart_tic() in Initial_temperature.c so that time is correctly
+ read in while using the lith_ages
+
+2006-06-02 23:38 gurnis
+
+ * lib/Full/Boundary_conditions.c, lib/Full/Lith_age.c,
+ lib/Regional/Boundary_conditions.c, lib/Regional/Lith_age.c:
+ Fixed bugs associated assimilating lith_age files into Full.
+ Slightly improved method of assimilating lith_age
+
+2006-05-18 18:05 cassie
+
+ * doc/manual/citcoms_book.xml: typo in manual corrected
+
+2006-05-16 19:50 cassie
+
+ * doc/manual/citcoms_book.xml: additional minor updates to manual
+
+2006-05-16 18:36 cassie
+
+ * doc/manual/citcoms_book.xml: minor updates to manual
+
+2006-04-18 23:34 luis
+
+ * lib/Full/Obsolete.c: Fixed typos.
+
+2006-03-28 19:22 walter
+
+ * .: Changed externals from svn:// to http://
+
+2006-02-14 23:24 leif
+
+ * ChangeLog, NEWS: Updated NEWS and ChangeLog.
+
+2006-02-14 22:24 leif
+
+ * pyre/SimpleApp.py, tests/Makefile.am, tests/citcomsfull.sh.in,
+ tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Merged
+ r2600 (fix for issue13, "make PYTHONPATH automatic") from v2
+ branch to trunk.
+
2006-02-04 02:11 luis
* doc/manual/citcoms_book.xml: Fixed about 20 assorted typos.
@@ -10,16 +2914,18 @@
2006-02-04 00:15 luis
* lib/Full/Version_dependent.c: The value of max_size needs to be
- larger by 1, or else we access out-of-bound array elements in
- the arrays E->boundary.element and E->boundary.normal. Refer to
- issue10 in roundup for more details.
+ larger by 1, or else we access out-of-bound array elements in the
+ arrays E->boundary.element and E->boundary.normal.
+
+ Refer to issue10 in roundup for more details.
2006-02-04 00:11 luis
* lib/Common/global_defs.h: Adjusted size of arrays in struct
- Shape_function_dA. This fixes a bug involving out-of-bounds
- array access caused by use of fortran-style indexing. Refer to
- issue10 in roundup for more information.
+ Shape_function_dA. This fixes a bug involving out-of-bounds array
+ access caused by use of fortran-style indexing.
+
+ Refer to issue10 in roundup for more information.
2006-02-04 00:04 luis
@@ -29,8 +2935,8 @@
2006-01-31 23:16 leif
- * pyre/Components/Launchers.py: Merged r2575 (fix for issue9,
- "need a property for extra LSF options") from v2 branch to trunk.
+ * pyre/Components/Launchers.py: Merged r2575 (fix for issue9, "need
+ a property for extra LSF options") from v2 branch to trunk.
2006-01-31 20:23 leif
@@ -89,8 +2995,8 @@
2005-11-04 19:39 leif
- * doc/manual/citcoms_book.xml: Regenerated PDF: updated date;
- minor corrections, format tweaks.
+ * doc/manual/citcoms_book.xml: Regenerated PDF: updated date; minor
+ corrections, format tweaks.
2005-11-03 00:26 tan2
@@ -118,9 +3024,8 @@
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook5/cookbook5.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook7/cookbook7.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/example1.sh,
- examples/Cookbook1/cookbook1.sh,
- examples/Cookbook2/cookbook2.sh: Set svn:executable on all
- examples and cookbooks.
+ examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh:
+ Set svn:executable on all examples and cookbooks.
2005-10-29 02:07 leif
@@ -180,13 +3085,11 @@
mc/3D/CitcomS/branches/v2/visual/visRegional.net.in,
mc/3D/CitcomS/branches/v2/visual/visRegionalSurface.net,
mc/3D/CitcomS/branches/v2/visual/visRegionalSurface.net.in,
- examples/Cookbook1/cookbook1.sh,
- examples/Cookbook2/cookbook2.sh,
- examples/Cookbook3/cookbook3.sh,
- examples/Cookbook4/cookbook4.sh,
- examples/Cookbook5/cookbook5.sh,
- examples/Cookbook7/cookbook7.sh, examples/example1.sh,
- visual/Makefile.am, visual/OpenDXMacro/CitcomSFullImport.net,
+ examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh,
+ examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.sh,
+ examples/Cookbook5/cookbook5.sh, examples/Cookbook7/cookbook7.sh,
+ examples/example1.sh, visual/Makefile.am,
+ visual/OpenDXMacro/CitcomSFullImport.net,
visual/OpenDXMacro/CitcomSFullImport.net.in,
visual/OpenDXMacro/CitcomSImport.net,
visual/OpenDXMacro/CitcomSImport.net.in,
@@ -432,47 +3335,43 @@
mc/3D/CitcomS/branches/v2/visual/getsurf.sh,
mc/3D/CitcomS/branches/v2/visual/parser.py,
mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh,
- mc/3D/CitcomS/branches/v2/visual/zslice.py, Make.mm,
- Makefile.am, configure.ac, drivers/Citcom.c,
- drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm,
- drivers/Makefile.am, drivers/Regional/Make.mm,
- drivers/Regional/local.def, drivers/local.def, etc/Make.mm,
- etc/Makefile.am, etc/__vault__.odb, etc/full-sphere.odb,
- etc/full.odb, etc/globus.odb, etc/incomp-newtonian.odb,
+ mc/3D/CitcomS/branches/v2/visual/zslice.py, Make.mm, Makefile.am,
+ configure.ac, drivers/Citcom.c, drivers/Full/Make.mm,
+ drivers/Full/local.def, drivers/Make.mm, drivers/Makefile.am,
+ drivers/Regional/Make.mm, drivers/Regional/local.def,
+ drivers/local.def, etc/Make.mm, etc/Makefile.am,
+ etc/__vault__.odb, etc/full-sphere.odb, etc/full.odb,
+ etc/globus.odb, etc/incomp-newtonian.odb,
etc/incomp-non-newtonian.odb, etc/lam-mpi.odb, etc/lsf.odb,
etc/mpich.odb, etc/pbs.odb, etc/regional-sphere.odb,
etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
- examples/Cookbook2/cookbook2.sh,
- examples/Cookbook3/cookbook3.sh,
- examples/Cookbook4/cookbook4.sh,
- examples/Cookbook5/cookbook5.sh,
+ examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
+ examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
examples/Cookbook7/cookbook7.sh, examples/Makefile.am,
examples/example1.sh, lib/Common/Advection_diffusion.c,
lib/Common/Citcom_init.c, lib/Common/Construct_arrays.c,
lib/Common/Convection.c, lib/Common/Drive_solvers.c,
lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c,
- lib/Common/Global_operations.c,
- lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
- lib/Common/Interuption.c, lib/Common/Make.mm,
- lib/Common/Makefile.am, lib/Common/Nodal_mesh.c,
- lib/Common/Obsolete.c, lib/Common/Output.c,
- lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c,
- lib/Common/Phase_change.c, lib/Common/Problem_related.c,
- lib/Common/Process_buoyancy.c, lib/Common/Shape_functions.c,
- lib/Common/Size_does_matter.c, lib/Common/Solver_conj_grad.c,
- lib/Common/Solver_multigrid.c, lib/Common/Sphere_harmonics.c,
- lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c,
- lib/Common/Tracer_advection.c,
+ lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
+ lib/Common/Instructions.c, lib/Common/Interuption.c,
+ lib/Common/Make.mm, lib/Common/Makefile.am,
+ lib/Common/Nodal_mesh.c, lib/Common/Obsolete.c,
+ lib/Common/Output.c, lib/Common/Pan_problem_misc_functions.c,
+ lib/Common/Parsing.c, lib/Common/Phase_change.c,
+ lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
+ lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c,
+ lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c,
+ lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c,
+ lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c,
lib/Common/Viscosity_structures.c, lib/Common/advection.h,
lib/Common/advection_diffusion.h, lib/Common/citcom_init.h,
lib/Common/convection_variables.h, lib/Common/drive_solvers.h,
lib/Common/element_definitions.h, lib/Common/global_defs.h,
lib/Common/initial_temperature.h, lib/Common/interuption.h,
- lib/Common/lith_age.h, lib/Common/local.def,
- lib/Common/output.h, lib/Common/parallel_related.h,
- lib/Common/parsing.h, lib/Common/phase_change.h,
- lib/Common/sphere_communication.h,
+ lib/Common/lith_age.h, lib/Common/local.def, lib/Common/output.h,
+ lib/Common/parallel_related.h, lib/Common/parsing.h,
+ lib/Common/phase_change.h, lib/Common/sphere_communication.h,
lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
lib/Common/viscosity_descriptions.h,
lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
@@ -571,10 +3470,10 @@
visual/Make.mm, visual/Makefile.am, visual/autocombine.py,
visual/batchcombine.py, visual/batchpaste.sh,
visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
- visual/dxgeneral.sh, visual/dxgeneralsurf.sh,
- visual/getcoord.sh, visual/getlog.sh, visual/getsurf.sh,
- visual/parser.py, visual/pasteCitcomData.sh, visual/zslice.py:
- Changed CitcomS license header text to GNU GPL.
+ visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
+ visual/getlog.sh, visual/getsurf.sh, visual/parser.py,
+ visual/pasteCitcomData.sh, visual/zslice.py: Changed CitcomS
+ license header text to GNU GPL.
2005-10-04 02:53 leif
@@ -585,8 +3484,7 @@
mc/3D/CitcomS/branches/v2/INSTALL,
mc/3D/CitcomS/branches/v2/Make.mm,
mc/3D/CitcomS/branches/v2/Makefile.am,
- mc/3D/CitcomS/branches/v2/NEWS,
- mc/3D/CitcomS/branches/v2/README,
+ mc/3D/CitcomS/branches/v2/NEWS, mc/3D/CitcomS/branches/v2/README,
mc/3D/CitcomS/branches/v2/citcoms_profile,
mc/3D/CitcomS/branches/v2/configure.ac,
mc/3D/CitcomS/branches/v2/drivers/Full/Make.mm,
@@ -738,9 +3636,9 @@
mc/3D/CitcomS/branches/v2/visual/getcoord.sh,
mc/3D/CitcomS/branches/v2/visual/getlog.sh,
mc/3D/CitcomS/branches/v2/visual/getsurf.sh,
- mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh,
- Makefile.am, tests/Make.mm: Ported GNU Build System from CitcomS
- trunk to v2 branch.
+ mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh, Makefile.am,
+ tests/Make.mm: Ported GNU Build System from CitcomS trunk to v2
+ branch.
2005-10-04 00:34 leif
@@ -751,8 +3649,8 @@
* ChangeLog: Strip "mc/3D/CitcomS/trunk" directory prefix. By the
way, this file is generated with svn2cl
- (http://ch.tudelft.nl/~arthur/svn2cl/) using the command "svn
- log --xml --verbose | xsltproc --stringparam strip-prefix
+ (http://ch.tudelft.nl/~arthur/svn2cl/) using the command "svn log
+ --xml --verbose | xsltproc --stringparam strip-prefix
mc/3D/CitcomS/trunk svn2cl.xsl - > ChangeLog".
2005-10-01 01:01 leif
@@ -788,18 +3686,19 @@
pyre/Makefile.am, pyre/SimpleApp.py, pyre/__init__.py,
pyre/__init__.py.in, tests/Make.mm, tests/Makefile.am,
tests/citcomsfull.sh.in, tests/citcomsregional.sh.in,
- tests/coupledcitcoms.sh.in: Add ${pythondir} to PYTHONPATH
- before checking for Python modules, so that installing multiple
- packages to a single PREFIX "just works". This also attempts to
- simulate the final installation environment, which might make a
- difference in unusual cases. Also, 'sed' the install-time
- PYTHONPATH into CitComS scripts (instead of an explicit list of
- @pythondir@'s). Added _getPrivateDepositoryLocations() and
- CitcomS.pml. Changed "etc/citcoms" to "etc/CitcomS" for
- consistency with the Python package name. Add PACKAGE_VERSION to
- __init__.py, and added pyconfig-generated config.py. Freeze the
- full path to 'mpirun' and 'mpipython.exe' at 'configure' time.
- First crack at batch system configuration.
+ tests/coupledcitcoms.sh.in: Add ${pythondir} to PYTHONPATH before
+ checking for Python modules, so that installing multiple packages
+ to a single PREFIX "just works". This also attempts to simulate
+ the final installation environment, which might make a difference
+ in unusual cases. Also, 'sed' the install-time PYTHONPATH into
+ CitComS scripts (instead of an explicit list of @pythondir@'s).
+
+ Added _getPrivateDepositoryLocations() and CitcomS.pml. Changed
+ "etc/citcoms" to "etc/CitcomS" for consistency with the Python
+ package name. Add PACKAGE_VERSION to __init__.py, and added
+ pyconfig-generated config.py. Freeze the full path to 'mpirun'
+ and 'mpipython.exe' at 'configure' time. First crack at batch
+ system configuration.
2005-09-21 00:03 leif
@@ -820,8 +3719,8 @@
lib/Full/Makefile.am, lib/Makefile.am, lib/Regional/Makefile.am,
module/Exchanger/Makefile.am, module/Full/Makefile.am,
module/Makefile.am, module/Regional/Makefile.am,
- pyre/Makefile.am, tests/Makefile.am, visual/Makefile.am: Added
- Id keyword property to configure.ac, Makefile.am.
+ pyre/Makefile.am, tests/Makefile.am, visual/Makefile.am: Added Id
+ keyword property to configure.ac, Makefile.am.
2005-09-09 19:41 leif
@@ -848,10 +3747,8 @@
etc/incomp-newtonian.odb, etc/incomp-non-newtonian.odb,
etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb, etc/pbs.odb,
etc/regional-sphere.odb, etc/regional.odb, etc/temp.odb,
- examples/Cookbook2/cookbook2.sh,
- examples/Cookbook3/cookbook3.sh,
- examples/Cookbook4/cookbook4.sh,
- examples/Cookbook5/cookbook5.sh,
+ examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
+ examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
examples/Cookbook7/cookbook7.sh, examples/example1.sh,
lib/Common/Element_calculations.c, lib/Common/Make.mm,
lib/Common/Obsolete.c, lib/Common/Size_does_matter.c,
@@ -928,23 +3825,23 @@
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/__init__.py,
pyre/Components/Tracer.py, pyre/Components/Visc.py,
- pyre/Components/__init__.py, pyre/CoupledApp.py,
- pyre/Coupler.py, pyre/Layout.py, pyre/Make.mm,
- pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
- pyre/Solver/Make.mm, pyre/Solver/RegionalSolver.py,
- pyre/Solver/Solver.py, pyre/Solver/__init__.py,
- pyre/__init__.py, pyre/local.def, tests/Make.mm,
- tests/array2d.cc, tests/asap.py, tests/citcomsfull.sh,
- tests/citcomsregional.sh, tests/coupledcitcoms.sh,
- tests/exchange.py, tests/hrothgar.py, tests/local.def,
- tests/signon.py, tests/test1.sh, tests/test2.sh, tests/test5.sh,
- visual/Make.mm, visual/autocombine.py, visual/batchcombine.py,
- visual/batchpaste.sh, visual/batchsurf.py, visual/combine.py,
- visual/combinesurf.py, visual/dxgeneral.sh,
- visual/dxgeneralsurf.sh, visual/getcoord.sh, visual/getlog.sh,
- visual/getsurf.sh, visual/miff2avi, visual/miff2mpg,
- visual/parser.py, visual/pasteCitcomData.sh, visual/zslice.py:
- Added executable property and 'Id' keyword expansion.
+ pyre/Components/__init__.py, pyre/CoupledApp.py, pyre/Coupler.py,
+ pyre/Layout.py, pyre/Make.mm, pyre/SimpleApp.py,
+ pyre/Solver/FullSolver.py, pyre/Solver/Make.mm,
+ pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
+ pyre/Solver/__init__.py, pyre/__init__.py, pyre/local.def,
+ tests/Make.mm, tests/array2d.cc, tests/asap.py,
+ tests/citcomsfull.sh, tests/citcomsregional.sh,
+ tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py,
+ tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh,
+ tests/test5.sh, visual/Make.mm, visual/autocombine.py,
+ visual/batchcombine.py, visual/batchpaste.sh,
+ visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
+ visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
+ visual/getlog.sh, visual/getsurf.sh, visual/miff2avi,
+ visual/miff2mpg, visual/parser.py, visual/pasteCitcomData.sh,
+ visual/zslice.py: Added executable property and 'Id' keyword
+ expansion.
2005-08-27 03:04 leif
@@ -952,11 +3849,10 @@
lib/Common/drive_solvers.h, lib/Common/global_defs.h,
lib/Common/output.h, lib/Common/parallel_related.h,
module/Regional/advdiffu.cc,
- module/Regional/initial_conditions.cc,
- module/Regional/mesher.cc, module/Regional/misc.cc,
- module/Regional/outputs.cc, module/Regional/stokes_solver.cc:
- Avoid 'extern "C" { #include ... }'; it causes problems with
- mpi++.h/mpicxx.h.
+ module/Regional/initial_conditions.cc, module/Regional/mesher.cc,
+ module/Regional/misc.cc, module/Regional/outputs.cc,
+ module/Regional/stokes_solver.cc: Avoid 'extern "C" { #include
+ ... }'; it causes problems with mpi++.h/mpicxx.h.
2005-07-27 08:58 leif
@@ -965,22 +3861,20 @@
invovled creating CitcomS's own version of LauncherMPICH, and
tweaking the MPI launchers so that CitcomS re-execs itself under
'mpipython.exe' when it is run under plain old 'python'. Also:
- made "--launcher.dry" work; ignore 'nodegen' in LauncherBatch
- (so that the examples "just work" on the TeraGrid); added some
- 'tips' ("--launcher.help-properties"); added SimpleApp.usage().
+ made "--launcher.dry" work; ignore 'nodegen' in LauncherBatch (so
+ that the examples "just work" on the TeraGrid); added some 'tips'
+ ("--launcher.help-properties"); added SimpleApp.usage().
2005-07-23 08:35 leif
* Make.mm, examples/Cookbook1/cookbook1.sh,
- examples/Cookbook2/cookbook2.sh,
- examples/Cookbook3/cookbook3.sh,
- examples/Cookbook4/cookbook4.sh,
- examples/Cookbook5/cookbook5.sh, examples/example1.sh,
- tests/Make.mm, tests/array2d.cc, visual/Make.mm: General build
- clean-up: 'export' all the various scripts to $EXPORT_ROOT/bin,
- so that goofy relative paths are not needed (e.g.,
- "../tests/citcomsregional.sh"); and so that the 'visual'
- directory doesn't have to be added to the PATH. I also
+ examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
+ examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
+ examples/example1.sh, tests/Make.mm, tests/array2d.cc,
+ visual/Make.mm: General build clean-up: 'export' all the various
+ scripts to $EXPORT_ROOT/bin, so that goofy relative paths are not
+ needed (e.g., "../tests/citcomsregional.sh"); and so that the
+ 'visual' directory doesn't have to be added to the PATH. I also
dusted-off 'array2d' -- it compiles and links now.
2005-07-23 08:00 leif
@@ -991,18 +3885,17 @@
2005-07-22 10:03 leif
- * pyre/Components/Launchers.py: Switched from Python's '%'
- operator to pyre.util.expandMacros(), so that I don't have to
- escape '%' (e.g., --launcher.nodegen="n%03d"). Also, export key
- environment variables to LAM/MPI jobs.
+ * pyre/Components/Launchers.py: Switched from Python's '%' operator
+ to pyre.util.expandMacros(), so that I don't have to escape '%'
+ (e.g., --launcher.nodegen="n%03d"). Also, export key environment
+ variables to LAM/MPI jobs.
2005-07-22 05:55 leif
* lib/Common/Make.mm, lib/Common/local.def, lib/Full/Make.mm,
- lib/Full/local.def, lib/Regional/Make.mm,
- lib/Regional/local.def: Build with soflags to produce
- position-independent code. 'Export' the resulting shared
- libraries.
+ lib/Full/local.def, lib/Regional/Make.mm, lib/Regional/local.def:
+ Build with soflags to produce position-independent code. 'Export'
+ the resulting shared libraries.
2005-07-20 04:23 leif
@@ -1013,10 +3906,9 @@
2005-07-20 04:12 leif
- * examples/ncsa.sh, examples/tacc.sh: Removed sample batch
- scripts, which are obsoleted by my new launchers. Use
- "--launcher=pbs" or "--launcher=lsf" on NCSA and TACC,
- respectively.
+ * examples/ncsa.sh, examples/tacc.sh: Removed sample batch scripts,
+ which are obsoleted by my new launchers. Use "--launcher=pbs" or
+ "--launcher=lsf" on NCSA and TACC, respectively.
2005-07-20 04:07 leif
@@ -1068,6 +3960,9 @@
* visual/autocombine.py: script to automatically read input
parameters from input file and call batchcombine.py
+
+2005-06-16 02:33 tan2
+
* visual/batchcombine.py: 1. moved parts of the script into
functions so that other scripts can import them. 2. raise
ValueError when the length of machinefile is not right
@@ -1095,35 +3990,32 @@
etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb,
etc/incomp-non-newtonian.odb, etc/regional-sphere.odb,
etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
- examples/Cookbook2/cookbook2.sh,
- examples/Cookbook3/cookbook3.sh,
- examples/Cookbook4/cookbook4.sh,
- examples/Cookbook5/cookbook5.sh,
+ examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
+ examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
examples/Cookbook7/cookbook7.sh, examples/example1.sh,
lib/Common/Advection_diffusion.c, lib/Common/Citcom_init.c,
lib/Common/Construct_arrays.c, lib/Common/Convection.c,
lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c,
- lib/Common/Global_operations.c,
- lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
- lib/Common/Interuption.c, lib/Common/Make.mm,
- lib/Common/Nodal_mesh.c, lib/Common/Obsolete.c,
- lib/Common/Output.c, lib/Common/Pan_problem_misc_functions.c,
- lib/Common/Parsing.c, lib/Common/Phase_change.c,
- lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
- lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c,
- lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c,
- lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c,
- lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c,
- lib/Common/Viscosity_structures.c, lib/Common/advection.h,
- lib/Common/advection_diffusion.h, lib/Common/citcom_init.h,
- lib/Common/convection_variables.h, lib/Common/drive_solvers.h,
- lib/Common/element_definitions.h, lib/Common/global_defs.h,
- lib/Common/initial_temperature.h, lib/Common/interuption.h,
- lib/Common/lith_age.h, lib/Common/local.def,
- lib/Common/output.h, lib/Common/parallel_related.h,
- lib/Common/parsing.h, lib/Common/phase_change.h,
- lib/Common/sphere_communication.h,
+ lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
+ lib/Common/Instructions.c, lib/Common/Interuption.c,
+ lib/Common/Make.mm, lib/Common/Nodal_mesh.c,
+ lib/Common/Obsolete.c, lib/Common/Output.c,
+ lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c,
+ lib/Common/Phase_change.c, lib/Common/Problem_related.c,
+ lib/Common/Process_buoyancy.c, lib/Common/Shape_functions.c,
+ lib/Common/Size_does_matter.c, lib/Common/Solver_conj_grad.c,
+ lib/Common/Solver_multigrid.c, lib/Common/Sphere_harmonics.c,
+ lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c,
+ lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c,
+ lib/Common/advection.h, lib/Common/advection_diffusion.h,
+ lib/Common/citcom_init.h, lib/Common/convection_variables.h,
+ lib/Common/drive_solvers.h, lib/Common/element_definitions.h,
+ lib/Common/global_defs.h, lib/Common/initial_temperature.h,
+ lib/Common/interuption.h, lib/Common/lith_age.h,
+ lib/Common/local.def, lib/Common/output.h,
+ lib/Common/parallel_related.h, lib/Common/parsing.h,
+ lib/Common/phase_change.h, lib/Common/sphere_communication.h,
lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
lib/Common/viscosity_descriptions.h,
lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
@@ -1137,13 +4029,12 @@
lib/Regional/Parallel_related.c,
lib/Regional/Read_input_from_files.c,
lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
- lib/Regional/local.def, lib/local.def,
- module/Full/Fullmodule.cc, module/Full/Make.mm,
- module/Full/local.def, module/Make.mm, module/Regional/Make.mm,
- module/Regional/Regionalmodule.cc, module/Regional/advdiffu.cc,
- module/Regional/advdiffu.h, module/Regional/bindings.cc,
- module/Regional/bindings.h, module/Regional/exceptions.cc,
- module/Regional/exceptions.h,
+ lib/Regional/local.def, lib/local.def, module/Full/Fullmodule.cc,
+ module/Full/Make.mm, module/Full/local.def, module/Make.mm,
+ module/Regional/Make.mm, module/Regional/Regionalmodule.cc,
+ module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
+ module/Regional/bindings.cc, module/Regional/bindings.h,
+ module/Regional/exceptions.cc, module/Regional/exceptions.h,
module/Regional/initial_conditions.cc,
module/Regional/initial_conditions.h, module/Regional/local.def,
module/Regional/mesher.cc, module/Regional/mesher.h,
@@ -1182,33 +4073,30 @@
pyre/Facilities/__init__.py, pyre/Layout.py, pyre/Make.mm,
pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
pyre/Solver/Make.mm, pyre/Solver/RegionalSolver.py,
- pyre/Solver/Solver.py, pyre/Solver/__init__.py,
- pyre/__init__.py, pyre/local.def, tests/Make.mm,
- tests/array2d.cc, tests/asap.py, tests/citcomsfull.sh,
- tests/citcomsregional.sh, tests/coupledcitcoms.sh,
- tests/exchange.py, tests/hrothgar.py, tests/local.def,
- tests/signon.py, tests/test1.sh, tests/test2.sh, tests/test5.sh,
- visual/batchcombine.py, visual/batchpaste.sh,
+ pyre/Solver/Solver.py, pyre/Solver/__init__.py, pyre/__init__.py,
+ pyre/local.def, tests/Make.mm, tests/array2d.cc, tests/asap.py,
+ tests/citcomsfull.sh, tests/citcomsregional.sh,
+ tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py,
+ tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh,
+ tests/test5.sh, visual/batchcombine.py, visual/batchpaste.sh,
visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
- visual/dxgeneral.sh, visual/dxgeneralsurf.sh,
- visual/getcoord.sh, visual/getlog.sh, visual/getsurf.sh,
- visual/parser.py, visual/pasteCitcomData.sh, visual/zslice.py:
- Added license text.
+ visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
+ visual/getlog.sh, visual/getsurf.sh, visual/parser.py,
+ visual/pasteCitcomData.sh, visual/zslice.py: Added license text.
2005-06-08 11:02 tan2
* examples/Cookbook5/cookbook5.sh: 1. subsitute 'staging' with
- 'launcher' as required by pythia-0.8 2. removed unneccesary
- input parameters
+ 'launcher' as required by pythia-0.8 2. removed unneccesary input
+ parameters
2005-06-08 08:55 leif
- * pyre/CoupledApp.py, pyre/SimpleApp.py,
- pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
- pyre/Solver/Solver.py: Port from pythia-0.4 to pythia-0.8,
- continued: use "factory=" instead of "default=" in facilities
- where appropriate. The scripts example1.sh and test5.sh seem to
- work now.
+ * pyre/CoupledApp.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
+ pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: Port from
+ pythia-0.4 to pythia-0.8, continued: use "factory=" instead of
+ "default=" in facilities where appropriate. The scripts
+ example1.sh and test5.sh seem to work now.
2005-06-06 06:41 tan2
@@ -1225,11 +4113,9 @@
etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb,
etc/incomp-non-newtonian.odb, etc/regional-sphere.odb,
etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
- examples/Cookbook2/cookbook2.sh,
- examples/Cookbook3/cookbook3.sh,
- examples/Cookbook4/cookbook4.sh,
- examples/Cookbook7/cookbook7.sh, examples/example1.sh,
- module/Exchanger/AreaWeightedNormal.cc,
+ examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
+ examples/Cookbook4/cookbook4.sh, examples/Cookbook7/cookbook7.sh,
+ examples/example1.sh, module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/Boundary.cc,
module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/CitcomSource.cc, module/Exchanger/Convertor.cc,
@@ -1264,8 +4150,8 @@
* lib/Regional/Version_dependent.c,
module/Regional/setProperties.cc, pyre/Components/IC.py: * If a
user doesn't specify "blob_center", assign [-999.,-999.,-999] as
- a default values in IC.py. * The real default values are
- assigned in setProperties.cc * The distance calculation in
+ a default values in IC.py. * The real default values are assigned
+ in setProperties.cc * The distance calculation in
"construct_tic_from_input" modified. * A bug in
non-dimensionalizing half_space_age fixed.
@@ -1429,8 +4315,8 @@
2005-05-25 08:22 tan2
- * visual/zslice.py: changed the hard-wire path (/usr/bin/python)
- to run-time dep. path
+ * visual/zslice.py: changed the hard-wire path (/usr/bin/python) to
+ run-time dep. path
2005-05-25 04:28 tan2
@@ -1451,20 +4337,23 @@
2005-05-24 05:00 ces74
* lib/Common/Initial_temperature.c,
- lib/Common/convection_variables.h,
- lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
+ lib/Common/convection_variables.h, lib/Regional/Sphere_related.c,
+ lib/Regional/Version_dependent.c,
module/Regional/setProperties.cc, pyre/Components/IC.py: * added
- new parameters to control a hot blob as temperature IC. - One
- can specify three parameters: 1. Coordinates(theta,fi,r) of the
- center. 2. Radius. 3. The amount of temperature
- increase/decrease within the blob. - Currently works only for
- the Regional version. - CitcomS variable name:
- convection.blob_center, convection.blob_radius,
- convection.blob_dT - Pyre parameter name: solver.ic.blob_center,
- solver.ic.blob_radius, solver.ic.blob_dT - it is required to set
- "solver.ic.tic_method=2" * the format of coordinates file has
- been modified. - "nsd=1" is not recognized as "%s%d" on some
- machine. - now it should be "nsd= 1" to be read as "%s %d".
+ new parameters to control a hot blob as temperature IC. - One can
+ specify three parameters: 1. Coordinates(theta,fi,r) of the
+ center. 2. Radius. 3. The amount of temperature increase/decrease
+ within the blob. - Currently works only for the Regional version.
+
+ - CitcomS variable name: convection.blob_center,
+ convection.blob_radius, convection.blob_dT - Pyre parameter name:
+ solver.ic.blob_center, solver.ic.blob_radius, solver.ic.blob_dT
+
+ - it is required to set "solver.ic.tic_method=2"
+
+ * the format of coordinates file has been modified. - "nsd=1" is
+ not recognized as "%s%d" on some machine. - now it should be
+ "nsd= 1" to be read as "%s %d".
2005-05-20 05:39 leif
@@ -1476,8 +4365,8 @@
2005-05-20 05:01 ces74
* module/Exchanger/initTemperature.cc: * added a new function for
- the initial temperature field. - called "hot_blob_lith" -
- Thermal boudnary layer on top + one hot bloc at the center.
+ the initial temperature field. - called "hot_blob_lith" - Thermal
+ boudnary layer on top + one hot bloc at the center.
2005-05-19 01:27 leif
@@ -1514,9 +4403,10 @@
* lib/Common/Make.mm, lib/Full/Make.mm, lib/Regional/Make.mm:
facelifted to work with new "config" repository (cvs -d
- :pserver:config at cvs.cacr.caltech.edu:/config co config). I think
- this will still work with the old config... Eh you may want to
- check.
+ :pserver:config at cvs.cacr.caltech.edu:/config co config).
+
+ I think this will still work with the old config... Eh you may
+ want to check.
2005-03-30 10:34 vlad
@@ -1541,8 +4431,8 @@
2005-03-09 06:24 vlad
- * lib/Common/Tracer_advection.c: The tracer code only works in
- root processor
+ * lib/Common/Tracer_advection.c: The tracer code only works in root
+ processor
2005-02-18 08:13 tan2
@@ -1570,14 +4460,13 @@
lib/Common/convection_variables.h: Added new input parameter:
tic_method. When it is 0 (default), the temperature is a linear
profile + perturbation at some layers. When it is 1, the
- temperature is isothermal (== bottom b.c.) + uniformly cold
- plate (thickness specified by 'half_space_age').
+ temperature is isothermal (== bottom b.c.) + uniformly cold plate
+ (thickness specified by 'half_space_age').
2005-02-05 02:51 ces74
* module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h,
- module/Exchanger/bindings.cc,
- module/Exchanger/inlets_outlets.cc,
+ module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: * bindings for the SInlet
class added. * setSBCFlag() method added to SInlet.
@@ -1704,6 +4593,9 @@
* lib/Common/global_defs.h: fixed a problem in function pointer
declaration
+
+2005-01-19 07:19 tan2
+
* drivers/Citcom.c: uncommented tracer module
2005-01-19 06:30 vlad
@@ -1762,9 +4654,9 @@
2005-01-05 06:57 tan2
* module/Exchanger/SVTInlet.cc: 1. uncommented the journal output
- 2. removed codes about 'upwind bc', as it is proved not
- accurate. 3. removed a call to my_tbc(), which is specific to my
- Hawaii plume model and sliped through the repository
+ 2. removed codes about 'upwind bc', as it is proved not accurate.
+ 3. removed a call to my_tbc(), which is specific to my Hawaii
+ plume model and sliped through the repository
2005-01-01 03:00 tan2
@@ -1774,8 +4666,8 @@
2004-12-31 09:03 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: fixed
- a bug when nprocz>1 and excludeTop or/add excludeBottom is
- turned on
+ a bug when nprocz>1 and excludeTop or/add excludeBottom is turned
+ on
2004-12-28 09:38 tan2
@@ -1790,9 +4682,9 @@
2004-12-03 04:23 tan2
- * pyre/CoupledApp.py, pyre/SimpleApp.py: 1. In findLayput(),
- assing self.controller 2. In CoupledApp, two controllers are
- created. So, two controllers can have different output interval
+ * pyre/CoupledApp.py, pyre/SimpleApp.py: 1. In findLayput(), assing
+ self.controller 2. In CoupledApp, two controllers are created.
+ So, two controllers can have different output interval
(monitoringFrequency).
2004-11-25 05:47 ces74
@@ -1801,10 +4693,11 @@
lib/Common/global_defs.h, module/Regional/setProperties.cc,
pyre/Components/Advection_diffusion/Advection_diffusion.py: * a
new parameter, "filter_temperature" created as a memeber of the
- "Control" structure. - if it's 1, the function filter() is
- called to reduce artifical diffusioin. - it's 1 by default. *
- The command line option for this parameter is "filter_temp" - it
- belongs to the "Advection_diffusion" class, which is
+ "Control" structure. - if it's 1, the function filter() is called
+ to reduce artifical diffusioin. - it's 1 by default.
+
+ * The command line option for this parameter is "filter_temp" -
+ it belongs to the "Advection_diffusion" class, which is
instantiated as "tsolver" in Solver.py. - Usage:
--solver.tsolver.filter_temp=True/False
@@ -1816,8 +4709,8 @@
2004-11-09 07:21 ces74
- * visual/miff2avi, visual/miff2mpg: * added appropriate credits
- for these scripts.
+ * visual/miff2avi, visual/miff2mpg: * added appropriate credits for
+ these scripts.
2004-11-07 08:41 ces74
@@ -1827,14 +4720,14 @@
2004-10-08 07:28 tan2
- * pyre/Solver/Solver.py: don't use exchanger.initTemperature()
- when restart (use disk file for IC)
+ * pyre/Solver/Solver.py: don't use exchanger.initTemperature() when
+ restart (use disk file for IC)
2004-10-08 07:25 tan2
* lib/Common/Process_buoyancy.c: disable writing out surface hear
- flux information, for processor on the surface usually don't
- have E->fp ready to use.
+ flux information, for processor on the surface usually don't have
+ E->fp ready to use.
2004-10-08 07:21 tan2
@@ -1850,19 +4743,18 @@
2004-10-08 07:18 tan2
* lib/Full/Boundary_conditions.c,
- lib/Regional/Boundary_conditions.c: 1.
- temperatures_conform_bcs() is version (Full/Regional) dependent.
- Make a function pointer for it. 2. get_bcs_id_for_residual() is
- version independent. Move to Common/Construct_arrays.c
+ lib/Regional/Boundary_conditions.c: 1. temperatures_conform_bcs()
+ is version (Full/Regional) dependent. Make a function pointer for
+ it. 2. get_bcs_id_for_residual() is version independent. Move to
+ Common/Construct_arrays.c
2004-10-08 07:11 tan2
* module/Exchanger/SVTInlet.cc, module/Exchanger/TInlet.cc,
- module/Exchanger/VTInlet.cc,
- module/Exchanger/initTemperature.cc: 1.
- temperatures_conform_bcs() is version (Full/Regional) dependent.
- Make a function pointer for it. 2. in initTemperature.cc, add
- several new functions of different IC.
+ module/Exchanger/VTInlet.cc, module/Exchanger/initTemperature.cc:
+ 1. temperatures_conform_bcs() is version (Full/Regional)
+ dependent. Make a function pointer for it. 2. in
+ initTemperature.cc, add several new functions of different IC.
2004-10-08 07:08 tan2
@@ -1883,8 +4775,8 @@
2004-09-22 07:16 ces74
- * visual/combinesurf.py: * fixed a bug related to the loop over
- the surface procs for each cap.
+ * visual/combinesurf.py: * fixed a bug related to the loop over the
+ surface procs for each cap.
2004-09-22 06:44 ces74
@@ -1899,8 +4791,8 @@
2004-08-08 05:08 tan2
* pyre/Components/Exchanger/Exchanger.py, pyre/Controller.py,
- pyre/Coupler.py, pyre/Solver/Solver.py: Synchronized when to
- save the result. During a coupled run, when one solver saves the
+ pyre/Coupler.py, pyre/Solver/Solver.py: Synchronized when to save
+ the result. During a coupled run, when one solver saves the
result, the other solver will save too.
2004-08-07 06:25 tan2
@@ -1915,8 +4807,8 @@
2004-08-07 05:47 tan2
- * pyre/Components/Exchanger/FineGridExchanger.py: VTOutlet was
- used in creatII, TOutlet is used now.
+ * pyre/Components/Exchanger/FineGridExchanger.py: VTOutlet was used
+ in creatII, TOutlet is used now.
2004-08-07 03:22 tan2
@@ -1952,8 +4844,8 @@
module/Exchanger/AreaWeightedNormal.h: * Change of
implementation. Now the weighted normal vectors are taken from
CitcomS' internal data (from boundary determinant
- E->boundary.det, this array has been throughly tested), no
- needto compute them again. Havn't tested.
+ E->boundary.det, this array has been throughly tested), no needto
+ compute them again. Havn't tested.
2004-07-28 01:14 tan2
@@ -1967,9 +4859,9 @@
2004-07-27 06:56 tan2
- * visual/batchcombine.py: * the 1st argument can be either the
- name of machine file or a quoted machine list(eg. 'n101 n102').
- * modified the doc string
+ * visual/batchcombine.py: * the 1st argument can be either the name
+ of machine file or a quoted machine list(eg. 'n101 n102'). *
+ modified the doc string
2004-07-09 01:15 tan2
@@ -1978,8 +4870,9 @@
lib/Regional/Read_input_from_files.c: Previousely, CitcomS would
abort running when age < -1 Ma. This behavior is not desirable.
The following fixes change the behavior so that CitcomS will
- assume age=0 when time has passed present day. 1.
- find_age_in_MY() returns negative age when time has passed
+ assume age=0 when time has passed present day.
+
+ 1. find_age_in_MY() returns negative age when time has passed
present day 2. changed how age is manipulated before reading
age-dependet files
@@ -2071,8 +4964,8 @@
2004-06-26 03:06 tan2
- * visual/visFull.cfg, visual/visFull.net: 1. show (reduced)
- surface grid 2. make rotating the Plane easier
+ * visual/visFull.cfg, visual/visFull.net: 1. show (reduced) surface
+ grid 2. make rotating the Plane easier
2004-06-26 01:50 tan2
@@ -2115,8 +5008,8 @@
visual/samples/fulltest.cap8.0,
visual/samples/fulltest.cap8.0.general,
visual/samples/fulltest.cap9.0,
- visual/samples/fulltest.cap9.0.general: added sample data file
- of CitcomS Full
+ visual/samples/fulltest.cap9.0.general: added sample data file of
+ CitcomS Full
2004-06-25 02:38 tan2
@@ -2124,10 +5017,10 @@
2005-08-23 03:32 unknown_user
- * examples/Full/Make.mm, examples/Full/local.def,
- examples/Make.mm, examples/Regional/Make.mm,
- examples/Regional/local.def, examples/local.def: [vcp] delete of
- edited revision with dead state
+ * examples/Full/Make.mm, examples/Full/local.def, examples/Make.mm,
+ examples/Regional/Make.mm, examples/Regional/local.def,
+ examples/local.def: [vcp] delete of edited revision with dead
+ state
2004-06-25 02:31 tan2
@@ -2161,13 +5054,13 @@
* visual/visRegional.cfg, visual/visRegional.net: 1. added integer
interactor to control the cutting dimension of Slab 2. made the
names of interactor more descriptive 3. set the min of slab
- cutting position to 0 4. set the min and max of slab Autocolor
- to 0 and 1, respectively
+ cutting position to 0 4. set the min and max of slab Autocolor to
+ 0 and 1, respectively
2004-06-09 00:40 tan2
- * module/Full/.cvsignore: tell cvs to ignore linked source codes
- in this directory
+ * module/Full/.cvsignore: tell cvs to ignore linked source codes in
+ this directory
2004-06-09 00:32 tan2
@@ -2177,8 +5070,8 @@
* visual/batchsurf.py, visual/combinesurf.py,
visual/dxgeneralsurf.sh, visual/getsurf.sh: scripts to get back
- and combine the surf file (containing x, y, topography,
- heatflux, vx, vy)
+ and combine the surf file (containing x, y, topography, heatflux,
+ vx, vy)
2004-06-08 08:32 tan2
@@ -2281,8 +5174,8 @@
2004-05-26 05:24 tan2
* visual/samples, visual/samples/regtest.cap0.0,
- visual/samples/regtest.cap0.0.general: added new sample files
- for visualization
+ visual/samples/regtest.cap0.0.general: added new sample files for
+ visualization
2004-05-25 07:29 tan2
@@ -2317,9 +5210,9 @@
2004-05-24 02:13 tan2
- * lib/Common/Pan_problem_misc_functions.c: 'side_sbc' is
- applicable in regional version only. add a sanity check here.
- also remove some (incorrect) conditional #include
+ * lib/Common/Pan_problem_misc_functions.c: 'side_sbc' is applicable
+ in regional version only. add a sanity check here. also remove
+ some (incorrect) conditional #include
2004-05-24 02:10 tan2
@@ -2336,14 +5229,14 @@
2004-05-19 04:21 ces74
* module/Exchanger/Make.mm, module/Exchanger/bindings.cc,
- module/Exchanger/inlets_outlets.cc: * bindings for VOutlet,
- which sends only the velocity to a sink.
+ module/Exchanger/inlets_outlets.cc: * bindings for VOutlet, which
+ sends only the velocity to a sink.
2004-05-19 04:18 ces74
* module/Exchanger/VOutlet.cc, module/Exchanger/VOutlet.h,
- module/Exchanger/inlets_outlets.h: * Binding for VOutlet
- created: this send only the velocity to a sink.
+ module/Exchanger/inlets_outlets.h: * Binding for VOutlet created:
+ this send only the velocity to a sink.
2004-05-19 04:15 ces74
@@ -2353,9 +5246,9 @@
2004-05-19 03:40 tan2
* visual/OpenDXMacro/ScaledGlyphs.net: macro that takes two data
- and plot them as two glyphs that has the same size (eg. length
- of arrow) scale. The shape (eg. the thickness of arrow) cannot
- be scaled automaticly though.
+ and plot them as two glyphs that has the same size (eg. length of
+ arrow) scale. The shape (eg. the thickness of arrow) cannot be
+ scaled automaticly though.
2004-05-19 03:38 tan2
@@ -2365,8 +5258,8 @@
2004-05-13 02:10 patrick
- * doc/Exchanger.doxyconf: * Updated the package name in the
- Doxygen docs
+ * doc/Exchanger.doxyconf: * Updated the package name in the Doxygen
+ docs
2004-05-13 02:05 tan2
@@ -2514,8 +5407,8 @@
2004-05-01 01:41 tan2
- * module/Exchanger/Sink.cc: added another self test. This test
- will make sure that every mesh node is interpolated.
+ * module/Exchanger/Sink.cc: added another self test. This test will
+ make sure that every mesh node is interpolated.
2004-04-30 05:19 tan2
@@ -2548,6 +5441,9 @@
2004-04-29 07:23 tan2
* pyre/Components/BC.py: side_sbcs default to False
+
+2004-04-29 07:23 tan2
+
* lib/Common/Instructions.c: E->control.side_sbcs default to 0
2004-04-29 07:21 tan2
@@ -2599,9 +5495,9 @@
* pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Outlet.py: add SVTOutlet and SVTInlet
- classes and their bindings. These classes are for
- CitcomS-CitcomS coupling, b.c. with temperature, normal velocity
- and shear traction
+ classes and their bindings. These classes are for CitcomS-CitcomS
+ coupling, b.c. with temperature, normal velocity and shear
+ traction
2004-04-16 07:03 tan2
@@ -2610,9 +5506,9 @@
module/Exchanger/SVTOutlet.h, module/Exchanger/bindings.cc,
module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: add SVTOutlet and SVTInlet
- classes and their bindings. These classes are for
- CitcomS-CitcomS coupling, b.c. with temperature, normal velocity
- and shear traction
+ classes and their bindings. These classes are for CitcomS-CitcomS
+ coupling, b.c. with temperature, normal velocity and shear
+ traction
2004-04-16 07:01 tan2
@@ -2621,9 +5517,10 @@
2004-04-16 01:39 tan2
* lib/Common/Topo_gravity.c,
- module/Exchanger/TractionInterpolator.cc: rearranged the order
- of stress vector so that it conforms with Hugh's convention | 1
- 4 5 | stress =| 4 2 6 | | 5 6 3 |
+ module/Exchanger/TractionInterpolator.cc: rearranged the order of
+ stress vector so that it conforms with Hugh's convention
+
+ | 1 4 5 | stress =| 4 2 6 | | 5 6 3 |
2004-04-16 01:35 tan2
@@ -2673,8 +5570,8 @@
2004-04-13 06:23 tan2
- * lib/Common/Element_calculations.c: modify get_elt_tr() so that
- it computes traction per side, not per element. Also, some minor
+ * lib/Common/Element_calculations.c: modify get_elt_tr() so that it
+ computes traction per side, not per element. Also, some minor
speed improvement.
2004-04-10 08:05 tan2
@@ -2690,11 +5587,10 @@
2004-04-10 07:49 tan2
- * lib/Common/Element_calculations.c,
- lib/Common/Size_does_matter.c: 1. change interface of
- construct_side_c3x3matrix_el(): NS, far is replaced by side 2.
- in get_elt_tr(), traction is only imposed on top/bottom sides
- (will relax this constraint later)
+ * lib/Common/Element_calculations.c, lib/Common/Size_does_matter.c:
+ 1. change interface of construct_side_c3x3matrix_el(): NS, far is
+ replaced by side 2. in get_elt_tr(), traction is only imposed on
+ top/bottom sides (will relax this constraint later)
2004-04-10 07:00 tan2
@@ -2723,8 +5619,8 @@
2004-04-10 02:05 tan2
- * lib/Common/Element_calculations.c: fixed a bug in calculating
- RHS force vector due to boundary velocity
+ * lib/Common/Element_calculations.c: fixed a bug in calculating RHS
+ force vector due to boundary velocity
2004-04-10 01:39 tan2
@@ -2757,10 +5653,10 @@
2004-03-29 07:22 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
- pyre/Components/Exchanger/FineGridExchanger.py: usage of
- VTOutlet and VTInlet is replaced by TractionInlet and
- TractionOutlet. Goal: impose normal velocity and shear traction
- as bounary conditions
+ pyre/Components/Exchanger/FineGridExchanger.py: usage of VTOutlet
+ and VTInlet is replaced by TractionInlet and TractionOutlet.
+ Goal: impose normal velocity and shear traction as bounary
+ conditions
2004-03-29 07:20 tan2
@@ -2774,8 +5670,8 @@
module/Exchanger/TractionOutlet.h,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h,
- module/Exchanger/exchangers.cc: 1. TractionOutlet c'tor has a
- new argument to specify 'mode'. Avaiable modes are: 'F': send
+ module/Exchanger/exchangers.cc: 1. TractionOutlet c'tor has a new
+ argument to specify 'mode'. Avaiable modes are: 'F': send
traction only 'V": send velocity only (this is somewhat
duplicated with VTOutlet) 'FV": send both traction and velocity
2. TractionSource and TractionInterpolateor have to know how to
@@ -2786,6 +5682,9 @@
* module/Exchanger/bindings.cc: add bindings to TractionOutlet and
TractionInlet
+
+2004-03-29 07:05 tan2
+
* module/Exchanger/Make.mm, module/Exchanger/TractionInlet.cc,
module/Exchanger/TractionInlet.h,
module/Exchanger/inlets_outlets.cc,
@@ -2804,18 +5703,18 @@
2004-03-27 08:04 tan2
- * lib/Common/Element_calculations.c: 1. extract repeated codes to
- a new function add_force() 2. remove unused variables 3. add new
- function to compute RHS of momemtum eqn due to traction b.c.
- (not finished yet)
+ * lib/Common/Element_calculations.c: 1. extract repeated codes to a
+ new function add_force() 2. remove unused variables 3. add new
+ function to compute RHS of momemtum eqn due to traction b.c. (not
+ finished yet)
2004-03-27 07:42 tan2
- * lib/Common/Size_does_matter.c: 1. move
- get_global_1d_shape_fn_1() form Size_does_matter.c to Obsolete.c
- 2. add new function construct_bdry_det() to compute (6-side)
- surface determinant of boundary element 3. isolate some repeated
- codes to new function get_x_cart()
+ * lib/Common/Size_does_matter.c: 1. move get_global_1d_shape_fn_1()
+ form Size_does_matter.c to Obsolete.c 2. add new function
+ construct_bdry_det() to compute (6-side) surface determinant of
+ boundary element 3. isolate some repeated codes to new function
+ get_x_cart()
2004-03-27 07:41 tan2
@@ -2827,6 +5726,9 @@
* lib/Common/element_definitions.h: add a section defines the
ordering of the 6 surfaces of a element and the ordering of 4
nodes within each surface
+
+2004-03-27 07:39 tan2
+
* lib/Common/global_defs.h: add definition of new structure Bdry
and declaration of E->boundary. This structure is used to mark
boundary element and store its (6-side) surface determinants
@@ -2890,12 +5792,15 @@
2004-03-13 07:05 tan2
* lib/Common/Topo_gravity.c: restructure function get_STD_topo()
+
+2004-03-13 07:05 tan2
+
* lib/Common/Output.c: bug fix
2004-03-13 07:01 tan2
- * lib/Common/Output.c: isolate calculation and output of
- horizontal average into one function
+ * lib/Common/Output.c: isolate calculation and output of horizontal
+ average into one function
2004-03-12 07:25 tan2
@@ -2905,8 +5810,7 @@
2004-03-12 07:23 tan2
- * module/Exchanger/bindings.cc,
- module/Exchanger/inlets_outlets.cc,
+ * module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: simplified bindings to inlets
and outlets
@@ -2959,11 +5863,10 @@
* module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h,
module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h,
- module/Exchanger/bindings.cc,
- module/Exchanger/inlets_outlets.cc,
- module/Exchanger/inlets_outlets.h: 1. move attributes 'fge_t'
- and 'cge_t', methods 'storeTimestep' and 'getFactor' from
- VTInlet to Inlet. 2. change the binding accordingly
+ module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
+ module/Exchanger/inlets_outlets.h: 1. move attributes 'fge_t' and
+ 'cge_t', methods 'storeTimestep' and 'getFactor' from VTInlet to
+ Inlet. 2. change the binding accordingly
2004-02-27 07:04 tan2
@@ -2978,6 +5881,9 @@
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: use Inlet and
Outlet
+
+2004-02-27 06:29 tan2
+
* pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Make.mm,
pyre/Components/Exchanger/Outlet.py: add various classes for
@@ -3012,6 +5918,9 @@
2004-02-26 07:07 tan2
* module/Exchanger/Make.mm: add AbstractSource.cc
+
+2004-02-26 07:07 tan2
+
* module/Exchanger/AbstractSource.cc,
module/Exchanger/AbstractSource.h,
module/Exchanger/TractionSource.cc,
@@ -3055,8 +5964,8 @@
2004-02-25 04:26 tan2
* module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h: class
- which consuming nodal velocities and temperature, replacing
- (part of) BoundaryConditionSink class.
+ which consuming nodal velocities and temperature, replacing (part
+ of) BoundaryConditionSink class.
2004-02-25 04:24 tan2
@@ -3093,8 +6002,8 @@
2004-02-07 07:28 tan2
- * lib/Common/Output.c: increase number of digits for coordinate
- and viscosity output
+ * lib/Common/Output.c: increase number of digits for coordinate and
+ viscosity output
2004-02-06 04:17 tan2
@@ -3161,6 +6070,9 @@
2004-01-21 08:13 puru
* module/Exchanger/InteriorImposing.cc: A typo has been corrected
+
+2004-01-21 08:13 puru
+
* module/Exchanger/exchangers.cc: Corrected a typo
2004-01-21 06:57 tan2
@@ -3177,8 +6089,8 @@
2004-01-18 06:22 ces74
- * module/Exchanger/TractionInterpolator.cc: a bug fixed in
- traction calculation.
+ * module/Exchanger/TractionInterpolator.cc: a bug fixed in traction
+ calculation.
2004-01-17 10:10 puru
@@ -3210,14 +6122,15 @@
2004-01-15 09:04 ces74
* module/Exchanger/TractionInterpolator.cc: 1. in
- initComputeTraction, bbox is now boundedMesh.tightBBox(). 2.
- domain_cutout() causes a problem in Citcom. Until fixed, it's
+ initComputeTraction, bbox is now boundedMesh.tightBBox().
+
+ 2. domain_cutout() causes a problem in Citcom. Until fixed, it's
not called.
2004-01-15 08:48 tan2
- * visual/batchcombine.py: script to retrieve/combine Citcom data
- in OpenDX-friendly format
+ * visual/batchcombine.py: script to retrieve/combine Citcom data in
+ OpenDX-friendly format
2004-01-15 08:47 tan2
@@ -3230,9 +6143,8 @@
2004-01-15 07:22 tan2
* visual, visual/batchpaste.sh, visual/combine.py,
- visual/dxgeneral.sh, visual/getlog.sh,
- visual/pasteCitcomData.sh: add scripts to combine/retrieve
- Citcom data
+ visual/dxgeneral.sh, visual/getlog.sh, visual/pasteCitcomData.sh:
+ add scripts to combine/retrieve Citcom data
2004-01-15 03:07 tan2
@@ -3245,8 +6157,8 @@
2004-01-15 02:49 tan2
* module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h:
- add new method tightBBox() which returns a tight bounding box
- for current X_
+ add new method tightBBox() which returns a tight bounding box for
+ current X_
2005-08-23 03:26 unknown_user
@@ -3272,17 +6184,20 @@
module/Exchanger/TractionBC.h~,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h, module/Exchanger/bindings.cc,
- module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
- 1) New files TractionBC.cc TractionBC.h have been added. 2)
+ module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1)
+ New files TractionBC.cc TractionBC.h have been added. 2)
sendTraction is now a method of TractionSource.
2004-01-14 08:34 tan2
* module/Exchanger/initTemperature.cc: add function
basal_tbl_central_hot_blob()
- * module/Exchanger/Source.cc, module/Exchanger/Source.h:
- definition of destructor is moved from Source.h to Source.cc
+2004-01-14 08:34 tan2
+
+ * module/Exchanger/Source.cc, module/Exchanger/Source.h: definition
+ of destructor is moved from Source.h to Source.cc
+
2004-01-14 02:53 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
@@ -3293,9 +6208,9 @@
2004-01-13 11:55 tan2
* module/Exchanger/FEMInterpolator.cc,
- module/Exchanger/FEMInterpolator.h, module/Exchanger/misc.cc:
- new FEMInterpolator using every element nodes to do
- interpolation (was using 4 element nodes)
+ module/Exchanger/FEMInterpolator.h, module/Exchanger/misc.cc: new
+ FEMInterpolator using every element nodes to do interpolation
+ (was using 4 element nodes)
2004-01-13 11:01 ces74
@@ -3326,8 +6241,8 @@
2004-01-09 09:25 tan2
- * module/Exchanger/Convertor.cc: when unconverting,
- un-transformate first, then non-dimensionalize next.
+ * module/Exchanger/Convertor.cc: when unconverting, un-transformate
+ first, then non-dimensionalize next.
2004-01-09 08:38 ces74
@@ -3350,8 +6265,8 @@
2004-01-09 05:19 tan2
- * module/Exchanger/CartesianCoord.cc: 'Array2D: second index out
- of range' bug fixed
+ * module/Exchanger/CartesianCoord.cc: 'Array2D: second index out of
+ range' bug fixed
2005-08-23 03:25 unknown_user
@@ -3423,6 +6338,9 @@
2004-01-08 09:50 tan2
* module/Exchanger/exchangers.cc: bug fixed
+
+2004-01-08 09:50 tan2
+
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: typo fixed
@@ -3431,8 +6349,8 @@
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
- module/Exchanger/exchangers.h: 1. remove unnecessary functions
- in InteriorImposingSink and their bindings 2. convert/unconvert
+ module/Exchanger/exchangers.h: 1. remove unnecessary functions in
+ InteriorImposingSink and their bindings 2. convert/unconvert
temperature to standard/internal representation
2004-01-08 06:01 tan2
@@ -3447,13 +6365,13 @@
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
module/Exchanger/CartesianCoord.cc,
- module/Exchanger/CartesianCoord.h,
- module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h,
- module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
- module/Exchanger/Interpolator.cc, module/Exchanger/Make.mm,
- module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h,
- module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
- module/Exchanger/exchangers.h: 1. Convertor class will convert
+ module/Exchanger/CartesianCoord.h, module/Exchanger/Convertor.cc,
+ module/Exchanger/Convertor.h, module/Exchanger/Interior.cc,
+ module/Exchanger/Interior.h, module/Exchanger/Interpolator.cc,
+ module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
+ module/Exchanger/SIUnit.h, module/Exchanger/bindings.cc,
+ module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
+ Convertor class will convert
coordinate/velocity/traction/time/... from CitcomS' internal
representation to some standard representation (currently in SI
unit and Cartesian coordinate) 2. change other parts of code
@@ -3500,6 +6418,9 @@
2003-12-31 05:46 tan2
* module/Exchanger/BoundaryCondition.cc: temporary fix
+
+2003-12-31 05:46 tan2
+
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedMesh.cc,
module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc,
@@ -3537,8 +6458,8 @@
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
- pyre/Components/Exchanger/FineGridExchanger.py: Initial
- condition initialization has been done at a higher level
+ pyre/Components/Exchanger/FineGridExchanger.py: Initial condition
+ initialization has been done at a higher level
2003-12-23 08:42 puru
@@ -3550,9 +6471,9 @@
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
- pyre/Components/Exchanger/FineGridExchanger.py: all_variables
- has been moved from Exchanger to Finegrid and Coarsegrid
- Exchangers (for CitcomS-Snac Coupling)
+ pyre/Components/Exchanger/FineGridExchanger.py: all_variables has
+ been moved from Exchanger to Finegrid and Coarsegrid Exchangers
+ (for CitcomS-Snac Coupling)
2003-12-20 02:21 tan2
@@ -3582,9 +6503,9 @@
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/dimensionalization.h: 1) Added dimensionalize.h
which contains variables for dimensionalizing CitcomS variables
- 2) All variables sent out by Citcom exchanger are
- dimensionalized 3) All variables received in by Citcom exchanger
- are non-dimensionalized
+ 2) All variables sent out by Citcom exchanger are dimensionalized
+ 3) All variables received in by Citcom exchanger are
+ non-dimensionalized
2003-12-17 09:35 puru
@@ -3626,9 +6547,9 @@
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/TractionInterpolator.cc: Conevrsion from
- dimensional to non-dimensional and vice-versa 1) Forces have
- been dimensionalized in TractioInterpolator before sent to Snac
- 2) Velocities have been non-dimensionalized in InteriorImposing
+ dimensional to non-dimensional and vice-versa 1) Forces have been
+ dimensionalized in TractioInterpolator before sent to Snac 2)
+ Velocities have been non-dimensionalized in InteriorImposing
after receiving from Snac
2003-11-30 09:22 tan2
@@ -3658,6 +6579,9 @@
2003-11-29 06:32 ces74
* module/Exchanger/Interpolator.cc: interpolateF removed.
+
+2003-11-29 06:32 ces74
+
* module/Exchanger/Interpolator.h: interpolateF removed
2003-11-29 06:25 ces74
@@ -3667,14 +6591,15 @@
2003-11-29 06:23 ces74
- * module/Exchanger/exchangers.cc: new bindings added: PyObject *
- pyExchanger_sendTraction(PyObject *, PyObject *args) PyObject *
- pyExchanger_domain_cutout(PyObject *, PyObject *args)
+ * module/Exchanger/exchangers.cc: new bindings added:
+
+ PyObject * pyExchanger_sendTraction(PyObject *, PyObject *args)
+ PyObject * pyExchanger_domain_cutout(PyObject *, PyObject *args)
2003-11-29 06:21 ces74
- * module/Exchanger/bindings.cc: two entries added: sendTraction
- and domain_cutout
+ * module/Exchanger/bindings.cc: two entries added: sendTraction and
+ domain_cutout
2003-11-29 06:20 ces74
@@ -3691,14 +6616,16 @@
2003-11-29 06:19 ces74
- * module/Exchanger/Source.h: new functions defined: void
- interpolateF(Array2D<double,DIM>& F, All_variables* E) const;
- void domain_cutout(const All_variables* E) const;
+ * module/Exchanger/Source.h: new functions defined:
+
+ void interpolateF(Array2D<double,DIM>& F, All_variables* E)
+ const; void domain_cutout(const All_variables* E) const;
2003-11-29 06:18 ces74
- * module/Exchanger/Source.cc: new functions added: void
- Source::interpolateF() void Source::domain_cutout()
+ * module/Exchanger/Source.cc: new functions added:
+
+ void Source::interpolateF() void Source::domain_cutout()
2003-11-29 06:18 tan2
@@ -3715,8 +6642,9 @@
2003-11-29 06:16 ces74
* module/Exchanger/BoundaryCondition.cc: The body of the following
- functions are commented out: void
- BoundaryConditionSource::sendTraction() void
+ functions are commented out:
+
+ void BoundaryConditionSource::sendTraction() void
BoundaryConditionSource::domain_cutout()
2003-11-29 06:14 tan2
@@ -3731,8 +6659,8 @@
2003-11-27 07:27 tan2
- * drivers/Full/Make.mm, drivers/Regional/Make.mm: modify Make.mm
- so that it always make a new binary file
+ * drivers/Full/Make.mm, drivers/Regional/Make.mm: modify Make.mm so
+ that it always make a new binary file
2003-11-27 07:25 tan2
@@ -3753,8 +6681,8 @@
2003-11-27 05:24 tan2
- * lib/Full/Make.mm, lib/Regional/Make.mm: remove options related
- to library linking
+ * lib/Full/Make.mm, lib/Regional/Make.mm: remove options related to
+ library linking
2003-11-26 02:41 puru
@@ -3765,9 +6693,8 @@
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
- module/Exchanger/exchangers.h: Added facility (recvV) for
- CitcomS to receive velocity boundary condition in Snac-Citcom
- coupling
+ module/Exchanger/exchangers.h: Added facility (recvV) for CitcomS
+ to receive velocity boundary condition in Snac-Citcom coupling
2003-11-25 10:59 tan2
@@ -3784,6 +6711,9 @@
2003-11-25 05:37 ces74
* lib/Common/global_defs.h: traction[] array removed.
+
+2003-11-25 05:37 ces74
+
* lib/Common/Topo_gravity.c: populate E->gstress in get_STD_topo.
2003-11-25 05:26 ces74
@@ -3804,6 +6734,9 @@
* module/Exchanger/Interpolator.h: The prototype of "interpolateF"
added to the class "Interpolator" as a public member function.
+
+2003-11-25 05:03 ces74
+
* module/Exchanger/Source.h: The prototype of "interpolateF" added
to the class "Source" as a public member function.
@@ -3819,14 +6752,18 @@
2003-11-24 03:04 ces74
- * module/Exchanger/bindings.cc: "sendTraction" added to
- Exchanger's method table
+ * module/Exchanger/bindings.cc: "sendTraction" added to Exchanger's
+ method table
2003-11-24 02:25 ces74
* module/Exchanger/BoundaryCondition.cc: a typo fixed
+
+2003-11-24 02:25 ces74
+
* module/Exchanger/BoundaryCondition.cc:
BoundaryConditionSource::sendTraction() has been implemented.
+
This is for sending CitcomS' traction to other app as force BC.
2003-11-24 02:21 ces74
@@ -3834,8 +6771,10 @@
* module/Exchanger/BoundaryCondition.h: 1. A datamember, "fbc",
added to the class, "BoundaryConditionSource". 2. A public
memberfunction, "sendTraction()" added to
- "BoundaryConditionSource". These are for sending CitcomS'
- traction to other app. as force BC.
+ "BoundaryConditionSource".
+
+ These are for sending CitcomS' traction to other app. as force
+ BC.
2003-11-24 02:11 ces74
@@ -3852,20 +6791,20 @@
2003-11-24 02:02 ces74
- * module/Exchanger/Interpolator.cc: interpolateF added. This is
- for sending CitcomS' traction to other app's force BC.
+ * module/Exchanger/Interpolator.cc: interpolateF added. This is for
+ sending CitcomS' traction to other app's force BC.
2003-11-23 16:33 steve
* module/Regional/Make.mm: changed from $(TOOLS_DIR)/lib to
- $(TOOLS_LIBDIR) as the former is not always true (if you let
- pyre choose the export dir it will be in .../lib/Linux...)
+ $(TOOLS_LIBDIR) as the former is not always true (if you let pyre
+ choose the export dir it will be in .../lib/Linux...)
2003-11-23 16:31 steve
* module/Full/Make.mm: changed from $(TOOLS_DIR)/lib to
- $(TOOLS_LIBDIR) as the former is not always true (if you let
- pyre choose the export dir it will be in .../lib/Linux...)
+ $(TOOLS_LIBDIR) as the former is not always true (if you let pyre
+ choose the export dir it will be in .../lib/Linux...)
2003-11-22 07:15 tan2
@@ -3921,11 +6860,10 @@
module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
module/Exchanger/Interior.h, module/Exchanger/Make.mm,
module/Exchanger/Sink.h, module/Exchanger/Source.h,
- module/Exchanger/exchangers.cc,
- module/Exchanger/utilTemplate.cc,
+ module/Exchanger/exchangers.cc, module/Exchanger/utilTemplate.cc,
module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc,
- module/Exchanger/utility.h: 1. multi-processor
- AreaWeightedNormal 2. small improvements
+ module/Exchanger/utility.h: 1. multi-processor AreaWeightedNormal
+ 2. small improvements
2003-11-08 05:43 puru
@@ -4089,8 +7027,8 @@
2003-10-29 03:57 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. add
- sendSize(), receiveSize(), broadcastSize() and empty() methods
- 2. send(), receive(), and broadcast() will send/recieve size
+ sendSize(), receiveSize(), broadcastSize() and empty() methods 2.
+ send(), receive(), and broadcast() will send/recieve size
information and adjust its memory accordingly
2003-10-29 01:24 tan2
@@ -4125,6 +7063,9 @@
2003-10-28 09:51 tan2
* module/Exchanger/ExchangerClass.cc: change to Array2D.swap()
+
+2003-10-28 09:51 tan2
+
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1.
implementation changed: using vector as internal representation
2. swap() becomes a member function
@@ -4146,9 +7087,9 @@
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
- pyre/Components/Exchanger/__init__.py: 1. remove unsed
- attributes 'localLeader' 2. in __init__.py, factory methods now
- doesn't need any argument
+ pyre/Components/Exchanger/__init__.py: 1. remove unsed attributes
+ 'localLeader' 2. in __init__.py, factory methods now doesn't need
+ any argument
2005-08-23 03:19 unknown_user
@@ -4182,9 +7123,9 @@
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
- module/Exchanger/exchangers.cc: 1. add shrink() in Array2D 2.
- add shrinksize() in Boundary and Mapping 3. write (most) output
- via journal 4. remove unused attribute 'localLeader' in Exchanger
+ module/Exchanger/exchangers.cc: 1. add shrink() in Array2D 2. add
+ shrinksize() in Boundary and Mapping 3. write (most) output via
+ journal 4. remove unused attribute 'localLeader' in Exchanger
2003-10-24 02:06 puru
@@ -4199,8 +7140,10 @@
2003-10-23 03:33 ces74
* module/Exchanger/AreaWeightedNormal.cc: a bug fixed: in
- AreaWeightedNormal::imposeConstraint() if(outflow >
- toleranceOutflow_) ==> if (fabs(outflow) > toleranceOutflow_)
+ AreaWeightedNormal::imposeConstraint()
+
+ if(outflow > toleranceOutflow_) ==> if (fabs(outflow) >
+ toleranceOutflow_)
2003-10-22 08:15 tan2
@@ -4302,9 +7245,9 @@
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. add class 'Mapping' and its
- derived classes 'CoarseGridMapping' and 'FineGridMapping' 2.
- move 'bid2gid', 'bid2proc', 'bid2elem', and 'shape' from
- Boundary to Mapping 3. change Exchanger classes accordingly
+ derived classes 'CoarseGridMapping' and 'FineGridMapping' 2. move
+ 'bid2gid', 'bid2proc', 'bid2elem', and 'shape' from Boundary to
+ Mapping 3. change Exchanger classes accordingly
2003-10-11 07:35 tan2
@@ -4333,9 +7276,9 @@
2003-10-06 08:09 puru
- * module/Exchanger/Boundary.cc: Bug associated with round off
- error of degenerate case in fine grid node to Coarse grid
- element map has been fixed.
+ * module/Exchanger/Boundary.cc: Bug associated with round off error
+ of degenerate case in fine grid node to Coarse grid element map
+ has been fixed.
2003-10-06 07:53 puru
@@ -4352,8 +7295,8 @@
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: added method imposeConstraint
- to correct velocities which are consistent with
- incompressibility of the fluid.
+ to correct velocities which are consistent with incompressibility
+ of the fluid.
2003-10-04 21:24 puru
@@ -4374,10 +7317,10 @@
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1.
decompose init() to two functions initBound() and
- findBoundaryNodes() 2. remove init(), all of its functionality
- is done in mapFindGrid() 3. in mapCoarseGrid(), extend the
- domain when searching for node mapping 4. use auto_array_ptr for
- all member arrays to improve exception safety
+ findBoundaryNodes() 2. remove init(), all of its functionality is
+ done in mapFindGrid() 3. in mapCoarseGrid(), extend the domain
+ when searching for node mapping 4. use auto_array_ptr for all
+ member arrays to improve exception safety
2003-10-04 01:25 tan2
@@ -4397,9 +7340,9 @@
2003-10-04 01:12 tan2
- * module/Exchanger/FineGridExchanger.cc: 1. calculate
- boundary.size in a simplified way 2. remove call to
- boundary.init() (the job of init() is done in mapFindGrid() now)
+ * module/Exchanger/FineGridExchanger.cc: 1. calculate boundary.size
+ in a simplified way 2. remove call to boundary.init() (the job of
+ init() is done in mapFindGrid() now)
2003-10-04 01:10 tan2
@@ -4445,9 +7388,9 @@
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: 1. remove
- solverVelocities() 2. add preVSolverRun() and postVSolverRun()
- 3. add attribute 'toApplyBC' in FGE, which flags applying BC or
- not 4. print time marching information
+ solverVelocities() 2. add preVSolverRun() and postVSolverRun() 3.
+ add attribute 'toApplyBC' in FGE, which flags applying BC or not
+ 4. print time marching information
2003-09-30 09:02 puru
@@ -4484,8 +7427,8 @@
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
- module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
- 1. add attributes 'fge_t' and 'cge_t' in Exchanger class 2. init
+ module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
+ add attributes 'fge_t' and 'cge_t' in Exchanger class 2. init
'fge_t' and 'cge_t' in constructor 3. add functions
storeTimestep() in Exchanger class 4. add binding to
storeTimestep()
@@ -4516,6 +7459,9 @@
2003-09-30 03:22 tan2
* pyre/Coupler.py, pyre/Coupler/Coupler.py: bug fix
+
+2003-09-30 03:22 tan2
+
* module/Regional/setProperties.cc: bug in output fixed
2003-09-30 03:21 tan2
@@ -4567,6 +7513,9 @@
2003-09-29 04:44 tan2
* pyre/CoupledApp.py: change default coarse solver to full version
+
+2003-09-29 04:44 tan2
+
* pyre/Controller.py, pyre/Controller/Controller.py: pass
'totalTime' and 'steps' to endTimestep()
@@ -4580,10 +7529,9 @@
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
- module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
- 1. wait() and nowait() is replaced by exchangeSignal() 2. add
- helper functions exchangeInt(), exchangeDouble() and
- exchangeFloat()
+ module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
+ wait() and nowait() is replaced by exchangeSignal() 2. add helper
+ functions exchangeInt(), exchangeDouble() and exchangeFloat()
2003-09-29 03:41 tan2
@@ -4655,8 +7603,8 @@
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/exchangers.cc: 1. remove attribute 'lrank' in
- Exchanger class 2. 'rank' is processor rank in local
- communicator 3. modify Exchanger::createDataArray() and
+ Exchanger class 2. 'rank' is processor rank in local communicator
+ 3. modify Exchanger::createDataArray() and
Exchanger::deleteDataArray() 4. gather() and distribute() become
pure virtual functions 5. finish CGE::gather() 6. rename
interpolate() to interpretate() 7. modify CGE::interpretate()
@@ -4803,8 +7751,8 @@
2003-09-26 08:05 ces74
- * module/Exchanger/ExchangerClass.cc: ImposeBC now changes flags
- of boundary nodes.
+ * module/Exchanger/ExchangerClass.cc: ImposeBC now changes flags of
+ boundary nodes.
2003-09-26 05:47 ces74
@@ -4831,6 +7779,9 @@
* module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
CoarseGridExchanger.interpolateTemperature added
+
+2003-09-26 05:14 ces74
+
* module/Exchanger/bindings.cc:
CoarseGridExchanger.interpolateTemperature addedcc
@@ -4847,8 +7798,8 @@
2003-09-25 10:37 ces74
* module/Exchanger/Boundary.cc: theta_max, theta_min, fi_max,
- fi_min, ro ,ri were being redeclared as local variables -->
- fixed so that they are used only as members of boundary class.
+ fi_min, ro ,ri were being redeclared as local variables --> fixed
+ so that they are used only as members of boundary class.
2003-09-25 09:51 ces74
@@ -4882,9 +7833,10 @@
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
pyre/Components/Exchanger/FineGridExchanger.py,
- tests/exchange.py: 1. in Boundary.cc, bid2gid is now generated
- in a consistent way with assigning boundary.X arrays. 2. in
- ExchangerClass.cc, imposeBC method is added and tested.
+ tests/exchange.py: 1. in Boundary.cc, bid2gid is now generated in
+ a consistent way with assigning boundary.X arrays.
+
+ 2. in ExchangerClass.cc, imposeBC method is added and tested.
2003-09-22 05:24 ces74
@@ -4892,9 +7844,9 @@
module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
- module/Exchanger/ExchangerClass.cc,
- module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
- module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
+ module/Exchanger/ExchangerClass.cc, module/Exchanger/bindings.cc,
+ module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
+ module/Exchanger/misc.cc,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: All the functions needed by Exchanger are
@@ -4979,8 +7931,8 @@
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/FineGridExchanger.cc,
- module/Exchanger/FineGridExchanger.h: 1. change argument lists
- of createBoundary(), sendBoundary(), receiveBoundary() and
+ module/Exchanger/FineGridExchanger.h: 1. change argument lists of
+ createBoundary(), sendBoundary(), receiveBoundary() and
mapBoundary() 2. createBoundary(), sendBoundary(),
receiveBoundary() and mapBoundary() have passed test
@@ -4988,8 +7940,8 @@
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: 1. comment out send() and
- receive() declaration 2. change argument list of mapBoundary()
- 3. fix some bugs in sendVelocities() and receiveVelocities() 4.
+ receive() declaration 2. change argument list of mapBoundary() 3.
+ fix some bugs in sendVelocities() and receiveVelocities() 4.
comment out reset_target() 5. add some output in constructor
(commented out)
@@ -5013,8 +7965,8 @@
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
- pyre/Components/Exchanger/FineGridExchanger.py: findBoundary
- will not return boundary object
+ pyre/Components/Exchanger/FineGridExchanger.py: findBoundary will
+ not return boundary object
2003-09-12 04:32 tan2
@@ -5049,9 +8001,9 @@
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
- module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
- 1. finish exchangeTimestep(), wait() and nowait() to Exchanger,
- test passed 2. add skeleton of sendTemperature() and
+ module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
+ finish exchangeTimestep(), wait() and nowait() to Exchanger, test
+ passed 2. add skeleton of sendTemperature() and
receiveTemperature() to Exchanger 3. add bindings to the
functions above
@@ -5077,8 +8029,8 @@
pyre/Components/Exchanger/FineGridExchanger.py, pyre/Coupler.py,
pyre/Coupler/Coupler.py, pyre/Solver/Solver.py: 1. remove
exchanger.initialize() 2. change argument lists of
- initTemperature() and applyBoundaryConditions() 3. add more
- calls to Coupler in Solver
+ initTemperature() and applyBoundaryConditions() 3. add more calls
+ to Coupler in Solver
2003-09-10 03:57 tan2
@@ -5118,8 +8070,8 @@
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
- module/Exchanger/exchangers.h: 1. declare map() in Boundary
- class 2. changer argument list of several Exchanger functions
+ module/Exchanger/exchangers.h: 1. declare map() in Boundary class
+ 2. changer argument list of several Exchanger functions
2003-09-09 09:35 tan2
@@ -5132,9 +8084,9 @@
module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. move declartion and definition
- of Boundary class to seperated files (was in ExchangerClass.h)
- 2. add boundary creation and exchanging functions 3. add
- bindings to boundary creation and exchanging functions
+ of Boundary class to seperated files (was in ExchangerClass.h) 2.
+ add boundary creation and exchanging functions 3. add bindings to
+ boundary creation and exchanging functions
2003-09-09 09:28 tan2
@@ -5173,8 +8125,8 @@
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
- pyre/Components/Exchanger/FineGridExchanger.py:
- createExchanger() is done
+ pyre/Components/Exchanger/FineGridExchanger.py: createExchanger()
+ is done
2003-09-09 04:35 tan2
@@ -5253,27 +8205,32 @@
* examples/Regional/velbc/README,
examples/Regional/velbc/velbc_regional.tar.gz: 1. Velbc example
- files are now tarred and compressed. 2. README file explains how
- to untar the provided velbc archive and the naming scheme of the
- velbc files.
+ files are now tarred and compressed.
+
+ 2. README file explains how to untar the provided velbc archive
+ and the naming scheme of the velbc files.
2003-09-03 10:57 ces74
* examples/Full/input.sample, examples/Full/velbc,
examples/Full/velbc/README,
examples/Full/velbc/velbc_full.tar.gz: 1. input.sample has been
- modified to show how to read in velocity b.c. from files. 2. The
- gzipped tar file, velbc_full.tar.gz, contains velbc files for
- each M.Y. and for each sphereical cap. 3. README explains how to
- untar the velbc files and their naming scheme.
+ modified to show how to read in velocity b.c. from files.
+
+ 2. The gzipped tar file, velbc_full.tar.gz, contains velbc files
+ for each M.Y. and for each sphereical cap.
+
+ 3. README explains how to untar the velbc files and their naming
+ scheme.
2003-09-03 07:23 ces74
* examples/Regional/input.sample, examples/Regional/velbc,
examples/Regional/velbc/velbc_regional40,
examples/Regional/velbc/velbc_regional41: 1. The example input
- file is modified to show how to use velbc files. 2. velbc
- directory is added together with velbc examples.
+ file is modified to show how to use velbc files.
+
+ 2. velbc directory is added together with velbc examples.
2003-09-02 01:30 ces74
@@ -5281,18 +8238,26 @@
lib/Full/Read_input_from_files.c, lib/Regional/Make.mm,
lib/Regional/Read_input_from_files.c: 1. The function to read in
velocity boundary conditions for every My is removed from
- Common/Problem_related.c. 2. A new file, Read_input_from_files.c
- is added to lib/Full/ and lib/Regional/. This file contains a
- sinlge function 'read_input_files_for_timesteps'. 3.
- Full/Make.mm and Regional/Make.mm have been changed accordingly.
+ Common/Problem_related.c.
+
+ 2. A new file, Read_input_from_files.c is added to lib/Full/ and
+ lib/Regional/. This file contains a sinlge function
+ 'read_input_files_for_timesteps'.
+
+ 3. Full/Make.mm and Regional/Make.mm have been changed
+ accordingly.
2003-09-01 09:02 ces74
* drivers/Full/Make.mm, drivers/Regional/Make.mm: A bug fixed in
- the Makefiles: The rule for linking binaries, CitcomSFull and
- CitcomSRegional, had libCitcomSCommon.a and libCitcomSFull(or
- Regional).a as dependencies. --> now these are treated as
- libraries to which Citcom.o is linked.
+ the Makefiles:
+
+ The rule for linking binaries, CitcomSFull and CitcomSRegional,
+ had libCitcomSCommon.a and libCitcomSFull(or Regional).a as
+ dependencies.
+
+ --> now these are treated as libraries to which Citcom.o is
+ linked.
2005-08-23 03:10 unknown_user
@@ -5334,20 +8299,25 @@
2003-08-30 07:27 ces74
* pyre/Components/Param.py: The following five parameters are
- removed from the Param.inventory. minstep, maxstep, maxtotstep,
- storage_spacing, cpu_limits_in_seconds
+ removed from the Param.inventory.
+
+ minstep, maxstep, maxtotstep, storage_spacing,
+ cpu_limits_in_seconds
2003-08-30 07:24 ces74
- * drivers/Citcom.c: 1. A step is added to decide whether to
- proceed time-marching. 2. max_dimensionless_time is not a
- criterion for time-marching any more.
+ * drivers/Citcom.c: 1. A step is added to decide whether to proceed
+ time-marching.
+
+ 2. max_dimensionless_time is not a criterion for time-marching
+ any more.
2003-08-30 07:19 ces74
- * lib/Common/Advection_diffusion.c: The following parameters are
- no more used in PG_timestep_solve: minstep, maxstep, and
- maxtotstep
+ * lib/Common/Advection_diffusion.c: The following parameters are no
+ more used in PG_timestep_solve:
+
+ minstep, maxstep, and maxtotstep
2003-08-30 03:41 tan2
@@ -5398,8 +8368,8 @@
2003-08-29 06:18 ces74
- * pyre/Solver/Solver.py: bug fixed in the 'advance' method:
- tsolver and vsolver are now defined before being used.
+ * pyre/Solver/Solver.py: bug fixed in the 'advance' method: tsolver
+ and vsolver are now defined before being used.
2003-08-29 06:12 ces74
@@ -5415,9 +8385,9 @@
* pyre/Controller.py, pyre/Controller/Controller.py,
pyre/Controller/Make.mm, pyre/Controller/__init__.py,
pyre/Solver/Solver.py: 1. Controller.py modified:
- self.solver.start_simulation --> self.solver.launch 2. Solver.
- py modified: self.start_simulation --> self.launch 3. Make.mm
- and __init__.py added to CitcomS/pyre/Controller/
+ self.solver.start_simulation --> self.solver.launch 2. Solver. py
+ modified: self.start_simulation --> self.launch 3. Make.mm and
+ __init__.py added to CitcomS/pyre/Controller/
2003-08-29 05:53 ces74
@@ -5434,9 +8404,11 @@
* pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Solver/Solver.py: 1. Solver.py modified to be consistent
- with 'Controller'. 2. Advection_diffusion.py A new method,
- 'launch', runs PG_timestep_init(). The '_solve' method now
- executes only PG_timestep_solve()
+ with 'Controller'.
+
+ 2. Advection_diffusion.py A new method, 'launch', runs
+ PG_timestep_init(). The '_solve' method now executes only
+ PG_timestep_solve()
2005-08-23 03:09 unknown_user
@@ -5457,8 +8429,8 @@
2005-08-23 03:08 unknown_user
- * pyre/Components/Parallel.py: [vcp] delete of edited revision
- with dead state
+ * pyre/Components/Parallel.py: [vcp] delete of edited revision with
+ dead state
2003-08-28 03:52 tan2
@@ -5516,6 +8488,9 @@
pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/RegionalApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
pyre/Solver/Solver.py: fix bug introduced by previous check-in
+
+2003-08-23 05:35 tan2
+
* module/Regional/bindings.cc, module/Regional/setProperties.cc,
module/Regional/setProperties.h: fix typo
@@ -5612,14 +8587,17 @@
2003-08-16 01:59 tan2
- * lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h: ***
- empty log message ***
+ * lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h: *** empty
+ log message ***
2003-08-16 01:56 tan2
* module/Regional/bindings.cc, module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h: remove obsolete bindings to
general_stokes_solver_*()
+
+2003-08-16 01:56 tan2
+
* module/Regional/setProperties.cc,
module/Regional/setProperties.h: change function name:
pyCitcom_Stokes_solver_set_properties() ->
@@ -5672,14 +8650,17 @@
2003-08-13 03:43 ces74
- * drivers/Full/Make.mm, drivers/Regional/Make.mm: Modified in
- order to use separate static libraries: libCitcomSCommon.a,
- libCitcomSFull.a, and libCitcomSRegional.a
+ * drivers/Full/Make.mm, drivers/Regional/Make.mm: Modified in order
+ to use separate static libraries:
+
+ libCitcomSCommon.a, libCitcomSFull.a, and libCitcomSRegional.a
2003-08-13 03:40 ces74
- * lib/Common/Initial_temperature.c: Typo fixed: "Missing input
- parameter: 'perturbml' -> "Missing input parameter: 'perturbl'
+ * lib/Common/Initial_temperature.c: Typo fixed:
+
+ "Missing input parameter: 'perturbml' -> "Missing input
+ parameter: 'perturbl'
2003-08-12 23:54 ces74
@@ -5692,8 +8673,9 @@
lib/Regional/Make.mm, module/Full/Make.mm,
module/Regional/Make.mm: Makefiles in module/ and lib/ modified
to create three separate static libraries: libCitcomSCommon.a,
- libCitcomSFull.a, and libCitcomSRegional.a These libraries are
- used when linking *.so objects.
+ libCitcomSFull.a, and libCitcomSRegional.a
+
+ These libraries are used when linking *.so objects.
2003-08-10 03:25 tan2
@@ -5715,8 +8697,8 @@
2005-08-23 03:05 unknown_user
- * pyre/Components/Advection_diffusion/Temperature_diffadv.py:
- [vcp] delete of edited revision with dead state
+ * pyre/Components/Advection_diffusion/Temperature_diffadv.py: [vcp]
+ delete of edited revision with dead state
2003-08-09 05:13 tan2
@@ -5763,10 +8745,9 @@
* drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm,
drivers/Regional/Make.mm, drivers/Regional/local.def,
- drivers/local.def, lib/Common/Output.c,
- lib/Common/global_defs.h, lib/Full/Output.c,
- lib/Full/global_defs.h, lib/Full/lith_age.h, lib/Full/output.h,
- lib/Full/parallel_related.h, lib/Make.mm,
+ drivers/local.def, lib/Common/Output.c, lib/Common/global_defs.h,
+ lib/Full/Output.c, lib/Full/global_defs.h, lib/Full/lith_age.h,
+ lib/Full/output.h, lib/Full/parallel_related.h, lib/Make.mm,
lib/Regional/global_defs.h, lib/Regional/lith_age.h,
lib/Regional/output.h, lib/Regional/parallel_related.h,
lib/local.def: move header files global_defs.h, lith_age.h,
@@ -5774,9 +8755,9 @@
2003-08-07 04:09 tan2
- * lib/Common/Make.mm, lib/Full/Make.mm,
- lib/Full/Problem_related.c, lib/Regional/Make.mm,
- lib/Regional/Problem_related.c: unify Problem_related.c
+ * lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Problem_related.c,
+ lib/Regional/Make.mm, lib/Regional/Problem_related.c: unify
+ Problem_related.c
2003-08-07 04:00 tan2
@@ -5787,31 +8768,31 @@
lib/Regional/Initial_temperature.c, lib/Regional/Make.mm,
lib/Regional/Version_dependent.c,
lib/Regional/initial_temperature.h,
- module/Regional/setProperties.cc: unify Initial_temperature.c
- and initial_temperature.h
+ module/Regional/setProperties.cc: unify Initial_temperature.c and
+ initial_temperature.h
2003-08-07 01:56 tan2
- * lib/Common/Output.c, lib/Full/Obsolete.c, lib/Full/Output.c:
- move obsolete functions from Output.c to Obsolete.c
+ * lib/Common/Output.c, lib/Full/Obsolete.c, lib/Full/Output.c: move
+ obsolete functions from Output.c to Obsolete.c
2003-08-07 01:47 tan2
* lib/Common/Global_operations.c, lib/Common/Make.mm,
lib/Full/Global_operations.c, lib/Full/Make.mm,
lib/Full/Obsolete.c, lib/Regional/Global_operations.c,
- lib/Regional/Make.mm, lib/Regional/Obsolete.c: unify two
- versions of Global_operations.c, and put it to Common/
+ lib/Regional/Make.mm, lib/Regional/Obsolete.c: unify two versions
+ of Global_operations.c, and put it to Common/
2003-08-03 07:43 tan2
- * module/Regional/setProperties.cc: bug fixed,
- tests/citcomsfull.py now gives correct result
+ * module/Regional/setProperties.cc: bug fixed, tests/citcomsfull.py
+ now gives correct result
2003-08-02 05:57 tan2
- * tests/citcomsfull.py, tests/hrothgar.py: to run a Full version
- of CitcomS, use the following command: ./citcomsfull.py
+ * tests/citcomsfull.py, tests/hrothgar.py: to run a Full version of
+ CitcomS, use the following command: ./citcomsfull.py
--staging=hrothgar --param.datafile=/SOME_PATH/test
2005-08-23 03:02 unknown_user
@@ -5831,8 +8812,8 @@
module/Regional/setProperties.h,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h, module/local.def: make some
- changes in function names so that both Full and Regioanl
- versions can use the same source code.
+ changes in function names so that both Full and Regioanl versions
+ can use the same source code.
2005-08-23 03:02 unknown_user
@@ -5848,10 +8829,12 @@
module/Full/exceptions.cc, module/Full/exceptions.h,
module/Full/local.def, module/Full/misc.cc, module/Full/misc.h:
module/Full and module/Regional now use the same files, except
- $(TYPE)module.cc and Make.mm. ***** Important ***** When you
- check out this directory (module/Full) in the first time, do 'mm
- link' in this directory. This will hard-link every source files
- in module/Regional to this directory.
+ $(TYPE)module.cc and Make.mm.
+
+ ***** Important ***** When you check out this directory
+ (module/Full) in the first time, do 'mm link' in this directory.
+ This will hard-link every source files in module/Regional to this
+ directory.
2003-08-02 05:25 tan2
@@ -5863,9 +8846,8 @@
* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py,
pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/Make.mm,
pyre/RegionalApp.py, pyre/Solver/FullSolver.py,
- pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: 1. add
- base class CitcomApp 2. derive FullApp and RegionalApp form
- CitcomApp
+ pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: 1. add base
+ class CitcomApp 2. derive FullApp and RegionalApp form CitcomApp
2003-08-02 02:05 tan2
@@ -5873,8 +8855,8 @@
pyre/Components/Sphere/Make.mm,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
- pyre/Components/Sphere/__init__.py, pyre/Facilities/Mesher.py:
- 1. add a base class Sphere for component Sphere 2. add a new
+ pyre/Components/Sphere/__init__.py, pyre/Facilities/Mesher.py: 1.
+ add a base class Sphere for component Sphere 2. add a new
component FullSphere for Full version 3. change Make.mm,
__init__.py, and the binder of facility Mesher accordingly
@@ -5893,26 +8875,28 @@
2003-07-30 03:54 tan2
* drivers/Make.mm, lib/Make.mm: *** empty log message ***
+
+2003-07-30 03:54 tan2
+
* lib/Common/Output.c, lib/Common/Process_buoyancy.c,
lib/Full/Boundary_conditions.c, lib/Full/Global_operations.c,
lib/Full/Initial_temperature.c, lib/Full/Lith_age.c,
- lib/Full/Make.mm, lib/Full/Output.c,
- lib/Full/Parallel_related.c, lib/Full/Problem_related.c,
- lib/Full/Process_buoyancy.c, lib/Full/Version_dependent.c,
- lib/Full/global_defs.h, lib/Full/initial_temperature.h,
- lib/Full/lith_age.h, lib/Full/output.h,
- lib/Full/parallel_related.h: copy changes in Regional version to
- Full version
+ lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c,
+ lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c,
+ lib/Full/Version_dependent.c, lib/Full/global_defs.h,
+ lib/Full/initial_temperature.h, lib/Full/lith_age.h,
+ lib/Full/output.h, lib/Full/parallel_related.h: copy changes in
+ Regional version to Full version
2003-07-29 06:03 tan2
* pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Make.mm, pyre/Components/Sphere/Make.mm,
- pyre/Components/Stokes_solver/Make.mm,
- pyre/Facilities/Mesher.py, pyre/Facilities/TSolver.py,
- pyre/Facilities/VSolver.py, pyre/Make.mm, pyre/RegionalApp.py,
- pyre/Solver/RegionalSolver.py: change directory structures
+ pyre/Components/Stokes_solver/Make.mm, pyre/Facilities/Mesher.py,
+ pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py,
+ pyre/Make.mm, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py:
+ change directory structures
2003-07-29 04:57 tan2
@@ -5924,8 +8908,8 @@
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1.
- RegionalApp._setProperties() is called before Component.init()
- 2. some cosmetics
+ RegionalApp._setProperties() is called before Component.init() 2.
+ some cosmetics
2003-07-27 04:47 tan2
@@ -5968,8 +8952,7 @@
2003-07-25 03:10 tan2
- * lib/Common/Global_operations.c,
- lib/Regional/Global_operations.c,
+ * lib/Common/Global_operations.c, lib/Regional/Global_operations.c,
lib/Regional/Parallel_related.c, module/Regional/bindings.cc,
module/Regional/mesher.cc, module/Regional/mesher.h,
module/Regional/setProperties.cc, pyre/CitcomSRegional.py,
@@ -6044,26 +9027,31 @@
pyre/Components/IC.py, pyre/Components/Parallel.py,
pyre/Components/Param.py, pyre/Components/Phase.py,
pyre/Components/Visc.py: '*_set_prop' methods of the 'Regioanl'
- module are now called '*_set_properties'.
+ module are now called
+
+ '*_set_properties'.
2003-07-23 12:27 ces74
- * lib/Common/global_defs.h, lib/Regional/global_defs.h: New
- members of the "CONTROL" and the "All_variables" structure added.
+ * lib/Common/global_defs.h, lib/Regional/global_defs.h: New members
+ of the "CONTROL" and the "All_variables" structure added.
2003-07-23 12:26 ces74
* lib/Common/Initial_temperature.c,
lib/Regional/Initial_temperature.c: Originally local variables,
+
number_of_perturbations, perturb_ll, perturb_mm, load_depth, and
- perturb_mag, are now members of the global "All_variables"
- structure.
+ perturb_mag,
+
+ are now members of the global "All_variables" structure.
2003-07-23 12:22 ces74
* lib/Common/Parsing.c: Originally local variables, VERBOSE,
- DESCRIBE, and BEGINNER, are now global: members of the
- 'All_variables' structure.
+ DESCRIBE, and BEGINNER,
+
+ are now global: members of the 'All_variables' structure.
2003-07-23 12:19 ces74
@@ -6105,8 +9093,8 @@
* lib/Common/output.h, lib/Regional/Boundary_conditions.c,
lib/Regional/Obsolete.c, lib/Regional/Output.c,
- lib/Regional/Parallel_related.c, lib/Regional/output.h:
- partially eliminate use of static variables
+ lib/Regional/Parallel_related.c, lib/Regional/output.h: partially
+ eliminate use of static variables
2003-07-19 07:34 tan2
@@ -6125,20 +9113,19 @@
* lib/Common/Citcom_init.c, lib/Common/Drive_solvers.c,
lib/Common/Element_calculations.c,
- lib/Common/General_matrix_functions.c,
- lib/Common/Instructions.c, lib/Common/Interuption.c,
- lib/Common/Process_velocity.c, lib/Common/Solver_multigrid.c,
- lib/Common/Stokes_flow_Incomp.c, lib/Common/Tracer_advection.c,
- lib/Common/Viscosity_structures.c, lib/Common/citcom_init.h,
- lib/Common/interuption.h: 1. change Citcom_Init() to
- citcom_init() 2. add interuption.h, header file of Interuption.c
- 3. partially eliminate use of static variables
+ lib/Common/General_matrix_functions.c, lib/Common/Instructions.c,
+ lib/Common/Interuption.c, lib/Common/Process_velocity.c,
+ lib/Common/Solver_multigrid.c, lib/Common/Stokes_flow_Incomp.c,
+ lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c,
+ lib/Common/citcom_init.h, lib/Common/interuption.h: 1. change
+ Citcom_Init() to citcom_init() 2. add interuption.h, header file
+ of Interuption.c 3. partially eliminate use of static variables
2003-07-18 06:31 tan2
- * lib/Common/Global_operations.c,
- lib/Regional/Global_operations.c: vnorm_nonnewt() returned NaN
- if there was only one material type. bug? fixed.
+ * lib/Common/Global_operations.c, lib/Regional/Global_operations.c:
+ vnorm_nonnewt() returned NaN if there was only one material type.
+ bug? fixed.
2003-07-18 04:19 tan2
@@ -6153,8 +9140,8 @@
2003-07-17 04:49 tan2
* module/Regional/Make.mm, module/Regional/bindings.cc,
- module/Regional/mesher.cc, module/Regional/mesher.h: add
- bindings of component RegionalSphere()
+ module/Regional/mesher.cc, module/Regional/mesher.h: add bindings
+ of component RegionalSphere()
2005-08-23 02:55 unknown_user
@@ -6248,8 +9235,8 @@
2005-08-23 02:54 unknown_user
- * pyre/Components/Stokes_solver.py: [vcp] delete of edited
- revision with dead state
+ * pyre/Components/Stokes_solver.py: [vcp] delete of edited revision
+ with dead state
2003-07-10 02:42 tan2
@@ -6283,10 +9270,15 @@
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Advection_diffusion/Temperature_diffadv.py,
pyre/Components/Advection_diffusion/__init__.py: A component of
- "TSoler" facility added. Advection_diffusion.py is a general
- class of advection_diffusion solvers. Temperature_diffadv.py is
- a solver for temperature field. __init__.py exports
- temperature_diffadv under Advection_diffusion module.
+ "TSoler" facility added.
+
+ Advection_diffusion.py is a general class of advection_diffusion
+ solvers.
+
+ Temperature_diffadv.py is a solver for temperature field.
+
+ __init__.py exports temperature_diffadv under Advection_diffusion
+ module.
2003-07-04 06:40 ces74
@@ -6308,9 +9300,12 @@
pyre/Components/Stokes_solver/Incompressible.py:
ImcompressibleNonNewtonian() is inherited from
ImcompressibleNewtonian() now
- * pyre/Components/Stokes_solver/Stokes_solver.py: remove
- properties related to viscosity
+2003-06-27 06:14 tan2
+
+ * pyre/Components/Stokes_solver/Stokes_solver.py: remove properties
+ related to viscosity
+
2003-06-24 04:01 tan2
* pyre/Facilities/VSolver.py: bug fix
@@ -6371,8 +9366,8 @@
2003-05-24 00:58 tan2
- * tests/asap.py, tests/hrothgar.py: add two staging classes
- (copied from specfem_globe/tests/)
+ * tests/asap.py, tests/hrothgar.py: add two staging classes (copied
+ from specfem_globe/tests/)
2003-05-24 00:49 tan2
@@ -6394,8 +9389,8 @@
* lib/Common/Drive_solvers.c,
lib/Common/General_matrix_functions.c,
- lib/Common/Stokes_flow_Incomp.c, lib/Common/drive_solvers.h:
- test functions removed.
+ lib/Common/Stokes_flow_Incomp.c, lib/Common/drive_solvers.h: test
+ functions removed.
2003-05-23 11:47 ces74
@@ -6403,14 +9398,15 @@
lib/Common/General_matrix_functions.c,
lib/Common/Stokes_flow_Incomp.c,
lib/Common/advection_diffusion.h, lib/Common/drive_solvers.h:
- Fixed a bug related to deciding the validity of velocity
- solution in General_matrix_functions.c Functions reorganized for
- PG_timestep class.
+ Fixed a bug related to deciding the validity of velocity solution
+ in General_matrix_functions.c
+
+ Functions reorganized for PG_timestep class.
2003-05-23 11:22 ces74
- * pyre/Components/Advection_diffusion/Advection_diffusion.py:
- class PG_timestep now has only two methods: .init and .solve
+ * pyre/Components/Advection_diffusion/Advection_diffusion.py: class
+ PG_timestep now has only two methods: .init and .solve
2003-05-23 09:41 tan2
@@ -6478,9 +9474,9 @@
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Advection_diffusion/__init__.py,
- pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: A new
- package Advection_diffusion created. This package includes a new
- class, PG_timestep.
+ pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: A new package
+ Advection_diffusion created. This package includes a new class,
+ PG_timestep.
2003-05-23 01:17 ces74
@@ -6497,18 +9493,17 @@
module/Regional/outputs.h, pyre/CitcomSRegional.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. add class
CitcomOutput 2. add classes OutputCoord and OutputVelo, which
- write out coordinate and velocity output 3. add some functions
- in lib/Regional/Output.c for bindings 4. add python bindings to
- all above
+ write out coordinate and velocity output 3. add some functions in
+ lib/Regional/Output.c for bindings 4. add python bindings to all
+ above
2003-05-21 01:56 tan2
* pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Stokes_solver.py: 1. change
- implementation of Stokes_solver 2. change
- ImcompressibleNewtonian and ImcompressibleNonNewtonian
- accordingly
+ implementation of Stokes_solver 2. change ImcompressibleNewtonian
+ and ImcompressibleNonNewtonian accordingly
2003-05-21 01:55 tan2
@@ -6555,9 +9550,8 @@
lib/Regional/Global_operations.c,
lib/Regional/Parallel_related.c, lib/Regional/global_defs.h,
lib/Regional/parallel_related.h, module/Regional/misc.cc,
- tests/signon.py: 1. creat a new global variable
- E->parallel.world 2. replace all MPI_COMM_WORLD by
- E->parallel.world
+ tests/signon.py: 1. creat a new global variable E->parallel.world
+ 2. replace all MPI_COMM_WORLD by E->parallel.world
2003-04-30 03:14 tan2
@@ -6581,16 +9575,15 @@
* lib/Common/Problem_related.c, lib/Common/global_defs.h,
lib/Regional/Boundary_conditions.c,
- lib/Regional/Problem_related.c,
- lib/Regional/Version_dependent.c, lib/Regional/global_defs.h: 1.
- change 'control.mantle_temp' to 'control.lith_age_mantle_temp'
- 2. move functions deal with 'lith_age' to a 'Lith_age.c'
- (complete)
+ lib/Regional/Problem_related.c, lib/Regional/Version_dependent.c,
+ lib/Regional/global_defs.h: 1. change 'control.mantle_temp' to
+ 'control.lith_age_mantle_temp' 2. move functions deal with
+ 'lith_age' to a 'Lith_age.c' (complete)
2003-04-26 07:36 tan2
- * lib/Common/Element_calculations.c,
- lib/Common/Sphere_harmonics.c: bug fix in original code
+ * lib/Common/Element_calculations.c, lib/Common/Sphere_harmonics.c:
+ bug fix in original code
2003-04-26 05:58 tan2
@@ -6621,8 +9614,8 @@
2003-04-11 08:31 tan2
- * lib/Common/Citcom_init.c, module/Regional/misc.cc: clean up
- debug message
+ * lib/Common/Citcom_init.c, module/Regional/misc.cc: clean up debug
+ message
2003-04-11 08:27 ces74
@@ -6637,8 +9630,8 @@
2003-04-11 06:34 tan2
* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
- pyre/Solver/RegionalSolver.py: 1. add preInit() and postInit()
- 2. change EarthModelGrid to SimulationGrid
+ pyre/Solver/RegionalSolver.py: 1. add preInit() and postInit() 2.
+ change EarthModelGrid to SimulationGrid
2003-04-11 06:25 tan2
@@ -6704,8 +9697,8 @@
2003-04-04 08:42 tan2
* module/Regional/Make.mm, module/Regional/bindings.cc,
- module/Regional/misc.cc, module/Regional/misc.h,
- tests/signon.py: trial on binding of Citcom_Init(), not finished.
+ module/Regional/misc.cc, module/Regional/misc.h, tests/signon.py:
+ trial on binding of Citcom_Init(), not finished.
2003-04-04 08:41 tan2
@@ -6773,17 +9766,16 @@
lib/Common/Convection.c, lib/Common/Drive_solvers.c,
lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c,
- lib/Common/Global_operations.c,
- lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
- lib/Common/Make.mm, lib/Common/Nodal_mesh.c,
- lib/Common/Output.c, lib/Common/Pan_problem_misc_functions.c,
- lib/Common/Parsing.c, lib/Common/Phase_change.c,
- lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
- lib/Common/Process_velocity.c, lib/Common/Shape_functions.c,
- lib/Common/Size_does_matter.c, lib/Common/Solver_conj_grad.c,
- lib/Common/Solver_multigrid.c, lib/Common/Sphere_harmonics.c,
- lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c,
- lib/Common/Tracer_advection.c,
+ lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
+ lib/Common/Instructions.c, lib/Common/Make.mm,
+ lib/Common/Nodal_mesh.c, lib/Common/Output.c,
+ lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c,
+ lib/Common/Phase_change.c, lib/Common/Problem_related.c,
+ lib/Common/Process_buoyancy.c, lib/Common/Process_velocity.c,
+ lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c,
+ lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c,
+ lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c,
+ lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c,
lib/Common/Viscosity_structures.c, lib/Common/advection.h,
lib/Common/convection_variables.h,
lib/Common/element_definitions.h, lib/Common/global_defs.h,
@@ -6792,12 +9784,11 @@
lib/Common/viscosity_descriptions.h, lib/Full,
lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
lib/Full/Global_operations.c, lib/Full/Initial_temperature.c,
- lib/Full/Make.mm, lib/Full/Output.c,
- lib/Full/Parallel_related.c, lib/Full/Problem_related.c,
- lib/Full/Process_buoyancy.c, lib/Full/Sphere_related.c,
- lib/Full/Version_dependent.c, lib/Full/global_defs.h,
- lib/Full/local.def, lib/Make.mm, lib/Regional,
- lib/Regional/Boundary_conditions.c,
+ lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c,
+ lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c,
+ lib/Full/Sphere_related.c, lib/Full/Version_dependent.c,
+ lib/Full/global_defs.h, lib/Full/local.def, lib/Make.mm,
+ lib/Regional, lib/Regional/Boundary_conditions.c,
lib/Regional/Geometry_cartesian.c,
lib/Regional/Global_operations.c,
lib/Regional/Initial_temperature.c, lib/Regional/Make.mm,
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